User Guide to Semiempirical Tight Binding¶
This user guide focuses on the semiempirical quantum mechanical methods GFNn-xTB, their descendants, and corresponding composite schemes as implemented in the xtb (extended tight binding) program package.
We provide a number of detailed guides dealing with common task that can
be performed easily with the xtb program.
All guides are usually structured the same way, starting with some simple
examples using only the commandline and the default settings followed
by a trouble shooting section.
Detailed inputs are provided in a ready to use fashion to solve some
more special but still common tasks with xtb together with some
insights into the theory used behind the scences.
Recent developments, news and publications¶
2021-08-06 - QCxMS version 5.1.0 released
This new update of the QCxMS program <https://github.com/qcxms/QCxMS/releases/tag/v.5.1.0>_ changes the way xtb is used inside the code. Instead of a standalone implementation of xtb version 5.8.1 in the source code, we switched to using the tblite <https://github.com/awvwgk/tblite>_ library, which allows updates to the latest version of xtb. This, in return, leads to a significant increase in the computational speed of calculations done with the GFNn-xTB methods, while keeping the code independent from third party software.
Furhtermore, the PlotMS program <https://github.com/qcxms/PlotMS/releases/tag/v.5.1>_ has been updated as well.
2021-06-10 - xtb version 6.4.1 released
We released a new version of
xtbwith a significantly improved memory footprint for large scale calculations and improved parallelisation for frequency calculations. The parallel evaluation of hessians should with GFN-FF is now possible, overall we improved the stablility of the parallelisation which was slightly degraded in version 6.4.0. For xTB calculations the requiredOMP_STACKSIZEhas been significantly reduced by restructuring the integral evaluation slightly.Also, this version of
xtbnow supports the COSMO/CPCM solvation model using the ddPCM library.
2021-05-03 - DFT-D4 version 3.2.0 released
We released a new version of DFT-D4 further expanding the functionality of the Python API and the integration with QCEngine and ASE. In this process we simplified the installation of the Python extension module which should now also be possible with pip. The DFT-D4 program can now also calculate pairwise resolved dispersion energies, both for the pairwise additive and pairwise non-additive contributions to the total dispersion energy.
Find the complete release notes here.
xTB in Other Quantum Chemistry Programs¶
The xTB-methods are now officially available in other quantum chemistry programs!
in Orca 4.2 an IO-based interface to the
xtbbinary is availableAMS 2019 implements GFN1-xTB in their DFTB module
the entos program implements GFN1-xTB (also available in the webinterface)
the computational chemistry framework cuby4 supports
xtbTurbomole does support GFN1-xTB and GFN2-xTB since version 7.4
QCEngine supports calculations with the
xtbAPIthe GMIN, OPTIM, and PATHSAMPLE global optimization tools provide a
xtbinterfaceCP2K has an GFN1-xTB implementation since version 7.1
We missed your project here? No problem, just give us hint at the mailing list or open an issue at github.
Setup and Installation¶
This guide deal with the general setup and local installation of the xtb
program.
Contents
Getting the Program¶
There are several ways to obtain the xtb program.
Precompiled Binaries from GitHub¶
A precompiled version of the program can be obtained from the
latest release page
on GitHub.
To get the newest features an automatically generated
development version
is available for the latest commit on the default branch.
At the release page you find the a compressed tarball (tar xf xtb*.tar.xz)
usually containing the following content:
.
├── bin
│ └── xtb
├── include
│ └── xtb
│ └── xtb.h
├── lib
│ ├── libxtb.so -> libxtb.so.6
│ ├── libxtb.so.6 -> libxtb.so.6.3.1
│ ├── libxtb.so.6.3.1
│ └── pkgconfig
│ └── xtb.pc
└── share
├── man
│ ├── man1
│ │ └── xtb.1
│ └── man7
│ └── xcontrol.7
├── modules
│ └── modulefiles
│ └── xtb
│ └── 6.3.1
└── xtb
├── param_gfn2-xtb.txt
├── param_gfn1-xtb.txt
├── param_gfn0-xtb.txt
├── param_ipea-xtb.txt
└── .param_gfnff.xtb
The binary is usually compiled with the Intel Fortran compiler and statically
linked against Intel’s Math Kernel Library (Intel MKL).
Newer versions of xtb (6.2 and newer) additionally include a shared library,
the header specification of the C-API.
First check the version by
> xtb --version
-----------------------------------------------------------
| ===================== |
| x T B |
| ===================== |
| S. Grimme |
| Mulliken Center for Theoretical Chemistry |
| University of Bonn |
-----------------------------------------------------------
* xtb version 6.2.1 (bf8695d) compiled by 'ehlert@majestix' on 2019-10-25
normal termination of xtb
This should print some fancy banner, the version number, say 6.2.1, the
git commit hash, the user and host name of the programmer compiled the
program and at date.
Make sure the version is matching the version from the release page and
the commit hash is the actual commit hash of the release, also the date
of the compilation should match.
We compile the program on our clusters in Bonn, so the host name is usually
majestix (or hedy20 for the old-kernel version).
You get also the user name of the programmer drafting the release,
testing the binary and packing the tarball.
This line is very important when reporting a bug to us, because we can validate the binary you were using and easier reproduce it.
Installing with Conda¶
Note
To bootstrap a conda installation we recommend to either use the conda-forge distribution miniforge or the anaconda distribution miniconda.
Installing xtb from the conda-forge channel can be achieved by adding conda-forge to your channels with:
conda config --add channels conda-forge
Once the conda-forge channel has been enabled, xtb can be installed with:
conda install xtb
It is possible to list all of the versions of xtb available on your platform with:
conda search xtb --channel conda-forge
Note
The conda package manager can become quite slow when adding large channels like conda-forge, for a more performant alternative you can try to use mamba instead, which can be conveniently installed from the conda-forge channel with
conda install mamba -c conda-forge
Alternatively, the mambaforge installed can be used to bootstrap a conda installation with mamba preinstalled.
Setting up xtb¶
This section will give you the basic information you need to
know about the xtb program. Some of the steps are elemental
for your calculation to succeed, so please consider to follow
my instructions carefully.
Some part of the xtb program can be quite wasteful with stack memory,
to avoid stack overflows when calculating large molecules, you should
unlimit the system stack, e.g. with bash by
> ulimit -s unlimited
Note that the memory management of xtb is constantly improved to avoid
using large amounts of stack memory, but to be on the save side
include this option for production runs.
Parallelisation¶
The xtb program uses shared memory OpenMP parallelisation, to calculate larger systems
an appropriate OMP stacksize must be provided, chose a reasonable large number by
> export OMP_STACKSIZE=4G
Note
Note that the memory requirement will increase with the system size and the number of requested threads. Currently, for 3000 atom system each thread requires around 16GB of memory due to the usage of dense matrix algebra for the xTB Hamiltonian. You have to account for this by allowing an accordingly larger OpenMP stacksize.
To distribute the number of threads reasonable in the OpenMP section it is recommended to use
> export OMP_NUM_THREADS=<ncores>,1
You might want to deactivate nested OMP constructs by
> export OMP_MAX_ACTIVE_LEVELS=1
Tip
Most OpenMP regions allow to customize the scheduling by setting OMP_SCHEDULE,
for many threads the dynamic schedule has proven to give a good load-balance
between all threads.
The default linear algebra backend of xtb is the Math Kernel Library,
which usually comes as OpenMP threaded version and respects the settings
of OMP_NUM_THREADS. You can however still adjust the MKL parallelisation
separately by setting
> export MKL_NUM_THREADS=<ncores>
Environment Variables for xtb¶
A number of environment variables is used by xtb to perform calculations.
Please set the XTBPATH variable to include all locations were
you store information relevant for your xtb calculation, like configuration
files and parameter files.
The present working directory is implicitly included for most files that
are searched in the XTBPATH.
Environment Module¶
Note
Available since version 6.3.2
A tcl environment module is provided and can be used with usual module systems.
For installations from the tarball the prefix variable in the module file
has to be adjusted accordingly
--- ./share/modules/modulefiles/xtb/6.3.1
+++ ./share/modules/modulefiles/xtb/6.3.1
@@ -1,5 +1,5 @@
#%Module
-set prefix /
+set prefix /absolute/path/to/xtb
module-whatis "Semiempirical Extended Tight-Binding Program Package"
If the share/modules/modulesfiles directory is included in your MODULEPATH
you should be able to load xtb with
module load xtb
Important
If you plan to use the xtb shared library in your build system you have
to do a similar adjustment to the lib/pkgconfig/xtb.pc file.
Sourceable Shell Scripts¶
Example scripts to be sourced in your shells rc file are included in the distributed tarball:
source ./share/xtb/config_env.bash
and should setup all environment variables correctly in most cases.
Getting Help from xtb¶
Beside this manual you can check the in-program help by
> xtb --help
Unfortunately, this might be outdated,
therefore, you should refer to the man-pages distributed with the xtb program.
Please check for the man-pages of xtb(1) and xcontrol(7).
There is also an online documentation, but you already now that one, of course.
The Verbose Mode¶
If you think some information is missing in your calculation you can
switch to the verbose mode by using --verbose in the command line
arguments. This will increase the print level almost everywhere in the
xtb program, also the input parser will print a lot of information
that might be interesting for your current calculation.
Overall this can be an awful lot of information, so it is not recommended as a default option.
Using xTB with Orca¶
Orca 4.2 implements support for xTB calculations using an IO based interface
calling the xtb binary and parsing its output.
The binaries of Orca will call an executable called otool_xtb, which
should be placed in the directory containing the Orca binaries.
We recommend to create a symbolic link to your local xtb binary by
> ln -s $(which xtb) otool_xtb
Important
xtb version 6.2.3 produces an energy printout which cannot
be processes by the reader in Orca, to fix this issue, use
the provided script to wrap the xtb binary instead
of creating a symbolic link.
You can invoke xTB calculations in Orca by using one of the simple keywords
! XTB1 # for GFN1-xTB
! XTB2 # for GFN2-xTB
in your Orca input file, for more details refer to the Orca manual.
Orca will communicate with xtb mainly by using commandline arguments,
requesting singlepoint calculations and parsing the total energy and
gradient from the program output.
Of course you should setup the xtb related environment variables,
such that xtb can find its parameter files and configuration files.
The .xtbrc is still read if it is contained in XTBPATH and can
be used to change the behaviour of xTB calculations in Orca, e.g. for
setting the electronic temperature.
Quickstart into Production¶
This chapter should serve as a quickstart tutorial guiding you through your first
calculation employing the xTB methods.
As an example, the equilibrium geometry of a water molecule is calculated.
The description here is based on xtb version 6.2.2.
Contents
Note
The program can almost entirely controlled by the command-line, if you need more control you should resort to the Detailed Input file.
There are four main run types in xtb, most other run types are
composite types that try to provide convenient combinations from
those main run types.
Singlepoint Calculations¶
Independent of all other commands, there will always be a singlepoint
calculation carried out at the very beginning. To calculate something
xtb needs information about the molecular geometry and the kind
of atoms present.
The default input format is either the Turbomole coordinate file
as a $coord data group.
> cat coord
$coord
0.00000000000000 0.00000000000000 -0.73578586109551 o
1.44183152868459 0.00000000000000 0.36789293054775 h
-1.44183152868459 0.00000000000000 0.36789293054775 h
$end
> xtb coord
Like in Turbomole the coordinates can be given in Bohr (default)
or Ångström ($coord angs) or fractional coordinates ($coord frac).
Optional data groups like the systems periodicity ($periodic),
lattice parameters ($lattice [bohr|angs]) and cell parameters
($cell [bohr|angs]) can be provided as well.
The following input for a MgO crystal utilize this data groups:
$coord frac
0.00 0.00 0.00 mg
0.50 0.50 0.50 o
$periodic 3
$cell
5.798338236 5.798338236 5.798338236 60. 60. 60.
$end
Note
In previous version the coord data group had to start in the first line, this constraint has been relaxed by now.
Any valid xyz file can be used to provide coordinates and requires the
file extension .xyz. This format does not support periodic boundary conditions.
xtb also supports DFTB+ genFormat files (.gen), protein database files (.pdb)
mol-files (.mol) and structure-data files (.sdf), if the corresponding suffix
is encountered. Note that you cannot provide a mol file with the extension sdf.
Vasp’s POSCAR or CONTCAR files are read if the file is named as such.
By default xtb will search for .CHRG and .UHF files and obtain
from these the molecular charge and the number of unpaired electrons,
respectively. The molecular charge can also be specified by
> xtb molecule.xyz --chrg +1
which is equivalent to
> echo +1 > .CHRG && xtb molecule.xyz
This also works for the unpaired electrons as in
> xtb --uhf 2 input.sdf
Note that the position of the input coordinates is totally unaffected
by any command-line arguments, if you are not sure, whether xtb tries
to interpret your filename as flag use -- to stop the parsing
as command-line options for all following arguments.
> xtb -- -oh.xyz
To select the parametrization of the xTB method you can currently choose from three different geometry, frequency and non-covalent interactions (GFN) parametrization, which differ mostly in the cost–accuracy ratio,
> xtb --gfn 2 coord
to choose GFN2-xTB, which is also the default parametrization. Also available are GFN1-xTB, and GFN0-xTB.
Sometimes you might face difficulties converging the self consistent charge iterations, in this case it is usually a good idea to increase the electronic temperature and to restart at normal temperature
> xtb --etemp 1000.0 coord && xtb --restart coord
Geometry Optimizations¶
The main purpose of the xTB methods is to provide good geometries,
so the xtb comes with a build-in geometry optimizer, which usually
does a decent job. It is invoked by
> xtb coord --opt
> ls
coord xtbopt.coord xtbopt.log ...
The optimized coordinates is written to a new file (xtbopt.coord), which is
in the same format as the input geometry. You can view the geometry optimization
by opening the xtbopt.log with your favorite molecule viewer.
The log-file is in Xmol format and contains the current total energy
and the gradient norm in the comment line, gmolden usually works fine
for this.
A successful geometry optimization will print somewhere along the lines
*** GEOMETRY OPTIMIZATION CONVERGED AFTER 43 ITERATIONS ***
------------------------------------------------------------------------
total energy gain : -0.0094907 Eh -5.9555 kcal/mol
total RMSD : 0.7677834 a0 0.4063 Å
------------------------------------------------------------------------
after finishing the optimization procedures, while in all other cases that not exit in error
*** FAILED TO CONVERGE GEOMETRY OPTIMIZATION IN 500 ITERATIONS ***
will be printed, additionally a NOT_CONVERGED file is created in the
working directory, which might become handy for bulk jobs.
To get a geometry optimization to converge can be a hard job, usually the xTB methods can repair a lot, you might want to start from GFN0-xTB which does not have convergence issues and than improve with GFN2-xTB. Maybe you have to adjust the geometry by hand again, if even this fails.
xtb offers eight predefined levels for the geometry optimization,
which can be chosen by appending the level to the optimization flag as in
> xtb coord --opt tight
The thresholds defined by simple keywords are given here
level |
Econv/Eh |
Gconv/Eh·α⁻¹ |
Accuracy |
crude |
5 × 10⁻⁴ |
1 × 10⁻² |
3.00 |
sloppy |
1 × 10⁻⁴ |
6 × 10⁻³ |
3.00 |
loose |
5 × 10⁻⁵ |
4 × 10⁻³ |
2.00 |
lax |
2 × 10⁻⁵ |
2 × 10⁻³ |
2.00 |
normal |
5 × 10⁻⁶ |
1 × 10⁻³ |
1.00 |
tight |
1 × 10⁻⁶ |
8 × 10⁻⁴ |
0.20 |
vtight |
1 × 10⁻⁷ |
2 × 10⁻⁴ |
0.05 |
extreme |
5 × 10⁻⁸ |
5 × 10⁻⁵ |
0.01 |
The energy convergence (Econv) is the allowed change in the total energy at convergence, while the gradient convergence (Gconv) is the allowed change in the gradient norm at convergence. The accuracy is handed to the singlepoint calculations for integral cutoffs and self consistent field convergence criteria and is adjusted to fit the geometry convergence thresholds automatically.
The xTB methods are completely analytical, so you can in principle converge your results down to machine precision. Converging it down to the lower limit is more a development feature than a real life application but always possible.
Characterisation of Stationary Points¶
In xtb second derivatives are implemented by finite differences methods
(numerical second derivatives). Normally you want to calculate the Hessian
directly after a successful geometry optimization, this is done by using
> xtb coord --ohess
For the calculation on the input geometry use --hess instead.
Dealing with Small Imaginary Frequencies¶
For small imaginary modes xtb offers an automatic distortion feature
of these modes, say you have optimized a geometry and performed
a frequency calculation which leads to an imaginary frequency of
14 wavenumbers:
> xtb coord --ohess
...
-------------------------------------------------
| Frequency Printout |
-------------------------------------------------
projected vibrational frequencies (cm-1)
eigval : -0.00 -0.00 0.00 0.00 0.00 0.00
eigval : -14.26 8.12 9.26 12.09 15.85 17.73
eigval : 19.45 28.85 39.18 41.30 64.61 71.84
...
imag cut-off (cm-1) : 5.00
found 1 significant imaginary frequency
writing imag mode distorted coords to <xtbhess.coord>
for further optimization.
...
In this case xtb will generate a distorted structure, you can continue to
optimize with
> xtb xtbhess.coord --ohess
...
-------------------------------------------------
| Frequency Printout |
-------------------------------------------------
projected vibrational frequencies (cm-1)
eigval : -0.00 -0.00 -0.00 -0.00 0.00 0.00
eigval : 2.02 7.99 10.10 12.08 16.16 18.57
eigval : 23.88 28.93 38.35 42.18 64.86 73.76
...
The optimization will only take a few steps and the artifical imaginary frequency is gone after checking the frequency calculation.
Commandline Usage¶
For xtb we usually enjoy to build our workflows via commandline,
so most tasks can be performed without ever writing any kind of input file
(except for the geometry input, of course).
The man page can be found here.
Note
If you need more control you should resort to the Detailed Input file.
Contents
Runtypes¶
The most basic flags used in xtb are the runtypes. We have a bunch of
them, but many of the elaborate composite runtypes are constructed from
four basic runtypes: singlepoint (SP), geometry optimization (ANCopt),
frequency calculation (Hessian) and molecular dynamics (MD).
Every calculation performs the basic setup and at some (resonable) point
a property calculation.
- Singlepoint
- flag
--scc- description
just self-consistent charge (SCC) calculation. See Singlepoint Calculations for details.
- queue
setup, SP, properties
- Gradient
- flag
--grad- description
self-consistent charge (SCC) calculation, afterwards energy and gradient will be printed in a Turbomole readable format
- queue
setup, SP, properties
- Vertical IP
- flag
--vip- description
vertical ionisation potential (IP), calculates SCC on input structure and than removes an electron to perform another SCC calculation.
- queue
setup, SP, SP, properties
- Vertical EA
- flag
--vea- description
vertical electron affinity (EA), calculates SCC on input structure and than adds an electron to perform another SCC calculation.
- queue
setup, SP, SP, properties
- Vertical IP and EA
- flag
--vipea- description
both IP and EA are calculate by removing and adding an electron, respectively.
- queue
setup, SP, SP, SP, properties
- Global Electrophilicity Index
- flag
--vomega- description
global electrophilicity index from vertical IP and EA.
- queue
setup, SP, SP, SP, properties
- Fukui Indices
- flag
--vfukui- description
calculates Mulliken partial charges from the neutral, positive and negatively charged structure and calculates Fukui indices.
- queue
setup, SP, SP, SP, properties
- Electrostatic Potential
- flag
--esp- description
calculate electrostatic potential on VdW-grid
- queue
setup, SP, properties (with ESP calculation)
- STM picture
- flag
--stm- description
simulate a STM measurement (molecule should be aligned to xy-plane)
- queue
setup, SP, properties (with STM calculation)
- Geometry optimization
- flag
--opt- description
approximate normal coordinate optimization, performs an initial singlepoint calculation and a final singlepoint calculation on the optimized structure. See Geometry Optimization for details.
- queue
setup, SP, ANCopt, SP, properties
- Minimum Hopping
- flag
--metaopt- description
try to find conformers by geometry optimization, for each minimum located a bias potential is generated to push the optimizer to another local minimum.
- queue
setup, SP, ANCopt, SP, properties, ANCopt, …
- Guided Path Finder
- flag
--path [file]- description
apply a bias potential between the input and final geometry (from file) and force the geometry optimizer to generate a path between the two structures.
- queue
setup, SP, properties, ANCopt, …
- Modefollowing
- flag
--modef mode- description
follow
modewhich specifies the nth eigenmode from a previously done frequency calculation.- queue
setup, SP, properties, ANCopt, …
- Frequency calculation
- flag
--[o]hess- description
second derivative calculation, see Calculation of Vibrational Frequencies
- queue
setup, SP, [ANCopt, SP,] SP, Hessian, properties
- Molecular dynamics
- flag
--[o]md- description
molecular dynamics simulation, see Molecular Dyamics Simulations for details
- queue
setup, SP, [ANCopt, SP,] properties, MD
- Metadynamics
- flag
--metadyn [snapshots]- description
activates metadynamics simulation on start geometry, where
snapshotsis the number of structures from the trajectory should be used in the biasing potential. See Meta-Dynamics Simulations for details.- queue
setup, SP, properties, MD
- Simulated annealing
- flag
--siman- description
performs a number of simulated annealing steps on the input coordinates and tries to find a conformer ensemble. We recommend the CREST workflow (see Introduction to CREST) instead of this runtyp since it is faster and more reliable in finding the lowest conformer. This runtyp has been deprecated and removed in version 6.2!
- queue
setup, SP, properties, MD, ANCopt, …
Options¶
- -c, --chrg INT
specify molecular charge as INT, overrides
.CHRGfile andxcontroloption- -u, --uhf INT
specify Nalpha-Nbeta as INT, overrides
.UHFfile andxcontroloption- --gfn INT
specify parametrisation of GFN-xTB (default = 2)
- --etemp REAL
electronic temperature (default = 300K)
- -a, --acc REAL
accuracy for SCC calculation, lower is better (default = 1.0)
- --vparam FILE
Parameter file for vTB calculation
- –alpb SOLVENT [reference]
analytical linearized Poisson-Boltzmann (ALPB) model, available solvents are acetone, acetonitrile, aniline, benzaldehyde, benzene, ch2cl2, chcl3, cs2, dioxane, dmf, dmso, ether, ethylacetate, furane, hexandecane, hexane, methanol, nitromethane, octanol, woctanol, phenol, toluene, thf, water. The solvent input is not case-sensitive. The Gsolv reference state can be chosen as reference or bar1M (default).
- -g, –gbsa SOLVENT [reference]
generalized born (GB) model with solvent accessable surface (SASA) model, available solvents are acetone, acetonitrile, benzene (only GFN1-xTB), CH2Cl2, CHCl3, CS2, DMF (only GFN2-xTB), DMSO, ether, H2O, methanol, n-hexane (only GFN2-xTB), THF and toluene. The solvent input is not case-sensitive. The Gsolv reference state can be chosen as reference or bar1M (default).
- --cma
shifts molecule to center of mass and transforms cartesian coordinates into the coordinate system of the principle axis (not affected by
isotopes-file).- --pop
requests printout of Mulliken population analysis (done by default)
- --molden
requests printout of molden file
- --dipole
requests dipole printout (done by default)
- --wbo
requests Wiberg bond order printout (done by default)
- --lmo
requests localization of orbitals
- --fod
requests FOD calculation
- -I, --input FILE
use FILE as input source for
xcontrol(7)instructions- --namespace STRING
give this
xtb(1)run a namespace. All files, even temporary ones, will be named according to STRING.- --copy, --nocopy
copies the
xcontrolfile at startup (default = false)- --restart, --norestart
restarts calculation from
xtbrestart(default = true)- -P, --parallel INT
number of parallel processes
- --define
performs automatic check of input and terminate
- --citation
print citation and terminate
- --license
print license and terminate
- -v, --verbose
be more verbose (not supported in every unit)
- -s, --silent
clutter the screen less (not supported in every unit)
- --strict
turns all warnings into hard errors
- -h, --help
show help page
Geometry Input¶
Contents
Supported Geometry Formats¶
Currently the following input formats are supported by xtb.
Format |
Basename |
Suffix |
molecular |
periodic |
|---|---|---|---|---|
Turbomole |
coord |
coord, tmol |
x |
3D |
xyz file |
xyz |
x |
||
mol file |
mol |
x |
||
Structure-Data file |
sdf |
x |
||
Protein Database file |
pdb |
x |
||
Vasp’s POSCAR/CONTCAR |
poscar, contcar |
vasp, poscar, contcar |
3D |
|
genFormat |
gen |
x |
3D |
|
Gaussian external |
ein |
x |
Note
The default format is always Turbomole and neither the suffix nor the base name is case-sensitive for file type detection.
Turbomole Coordinate Input¶
The default input format is the Turbomole coordinate file as a $coord data
group.
$coord
0.00000000000000 0.00000000000000 -0.73578586109551 o
1.44183152868459 0.00000000000000 0.36789293054775 h
-1.44183152868459 0.00000000000000 0.36789293054775 h
$end
Like in Turbomole the coordinates can be given in Bohr (default)
or Ångström ($coord angs) or fractional coordinates ($coord frac).
Optional data groups like the systems periodicity ($periodic),
lattice parameters ($lattice [bohr|angs]) and cell parameters
($cell [bohr|angs]) can be provided as well.
The following input for a MgO crystal utilize this data groups:
$coord frac
0.00 0.00 0.00 mg
0.50 0.50 0.50 o
$periodic 3
$cell
5.798338236 5.798338236 5.798338236 60. 60. 60.
$end
Note
crest only supporting a plain coord data group without modifiers.
xyz Input¶
The well-known xyz or xmol format is supported by xtb as well.
The atom is identified by its element symbol and followed by its cartesian
coordinates in Ångström.
An example for caffeine is given with:
24
C 1.07317 0.04885 -0.07573
N 2.51365 0.01256 -0.07580
C 3.35199 1.09592 -0.07533
N 4.61898 0.73028 -0.07549
C 4.57907 -0.63144 -0.07531
C 3.30131 -1.10256 -0.07524
C 2.98068 -2.48687 -0.07377
O 1.82530 -2.90038 -0.07577
N 4.11440 -3.30433 -0.06936
C 5.45174 -2.85618 -0.07235
O 6.38934 -3.65965 -0.07232
N 5.66240 -1.47682 -0.07487
C 7.00947 -0.93648 -0.07524
C 3.92063 -4.74093 -0.06158
H 0.73398 1.08786 -0.07503
H 0.71239 -0.45698 0.82335
H 0.71240 -0.45580 -0.97549
H 2.99301 2.11762 -0.07478
H 7.76531 -1.72634 -0.07591
H 7.14864 -0.32182 0.81969
H 7.14802 -0.32076 -0.96953
H 2.86501 -5.02316 -0.05833
H 4.40233 -5.15920 0.82837
H 4.40017 -5.16929 -0.94780
mol and sdf Input¶
The mol and sdf format of the ct-file formats are partly supported in xtb.
Some limitations apply to those input formats are applied to those formats to
make them play nicely together with QM nature of the xTB methods.
This means not any mol or sdf input will be accepted as geometry input.
A valid sdf input is given for the water molecule with
Water
xtb 11041909383D
Comment line
3 2 0 0 0 999 V2000
-0.2191 -0.3098 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
0.7400 -0.2909 -0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
-0.5210 0.6007 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
1 3 1 0 0 0 0
M END
> <Formula>
H2 O
> <Mw>
18.01528
> <SMILES>
O([H])[H]
> <CSID>
937
$$$$
The input reader is strict in differentiating mol and sdf input, mol input with the sdf extension will be rejected by the reader. The topology and the sdf key-value pairs will be preserved and printed again in the final optimized geometry.
Multiple entries in an sdf input will be ignored by the reader.
Protein Database Input¶
The input reader supports parts of the pdb-format for reading single PDB file. Minimal sanity checks on the PDB input will be performed, i.e. the reader will outright reject any geometry without hydrogen atoms.
An valid example input (with hydrogen atoms and partial occupied sides removed) is given here:
ATOM 1 N GLY Z 1 -0.821 -2.072 16.609 1.00 9.93 N
ATOM 2 CA GLY Z 1 -1.705 -2.345 15.487 1.00 7.38 C
ATOM 3 C GLY Z 1 -0.968 -3.008 14.344 1.00 4.89 C
ATOM 4 O GLY Z 1 0.258 -2.982 14.292 1.00 5.05 O
ATOM 5 HA2 GLY Z 1 -2.130 -1.405 15.135 1.00 0.00 H
ATOM 6 HA3 GLY Z 1 -2.511 -2.999 15.819 1.00 0.00 H
ATOM 7 H1 GLY Z 1 -1.364 -1.742 17.394 1.00 0.00 H
ATOM 8 H2 GLY Z 1 -0.150 -1.365 16.344 1.00 0.00 H
ATOM 9 H3 GLY Z 1 -0.334 -2.918 16.868 1.00 0.00 H
ATOM 10 N ASN Z 2 -1.721 -3.603 13.425 1.00 3.53 N
ATOM 11 CA ASN Z 2 -1.141 -4.323 12.291 1.00 1.85 C
ATOM 12 C ASN Z 2 -1.748 -3.900 10.968 1.00 3.00 C
ATOM 13 O ASN Z 2 -2.955 -3.683 10.873 1.00 3.99 O
ATOM 14 CB ASN Z 2 -1.353 -5.827 12.446 1.00 5.03 C
ATOM 15 CG ASN Z 2 -0.679 -6.391 13.683 1.00 5.08 C
ATOM 16 OD1 ASN Z 2 0.519 -6.202 13.896 1.00 6.10 O
ATOM 17 ND2 ASN Z 2 -1.448 -7.087 14.506 1.00 8.41 N
ATOM 18 H ASN Z 2 -2.726 -3.557 13.512 1.00 0.00 H
ATOM 19 HA ASN Z 2 -0.070 -4.123 12.263 1.00 0.00 H
ATOM 20 HB2 ASN Z 2 -0.945 -6.328 11.568 1.00 0.00 H
ATOM 21 HB3 ASN Z 2 -2.423 -6.029 12.503 1.00 0.00 H
ATOM 22 HD21 ASN Z 2 -2.427 -7.218 14.293 1.00 0.00 H
ATOM 23 HD22 ASN Z 2 -1.056 -7.487 15.346 1.00 0.00 H
ATOM 24 N LEU Z 3 -0.907 -3.803 9.944 1.00 3.47 N
ATOM 25 CA LEU Z 3 -1.388 -3.576 8.586 1.00 3.48 C
ATOM 26 C LEU Z 3 -0.783 -4.660 7.709 1.00 3.29 C
ATOM 27 O LEU Z 3 0.437 -4.788 7.643 1.00 3.80 O
ATOM 28 CB LEU Z 3 -0.977 -2.185 8.081 1.00 3.88 C
ATOM 29 CG LEU Z 3 -1.524 -1.669 6.736 1.00 8.66 C
ATOM 30 CD1 LEU Z 3 -1.225 -0.191 6.570 1.00 9.89 C
ATOM 31 CD2 LEU Z 3 -0.962 -2.409 5.541 1.00 13.56 C
ATOM 32 H LEU Z 3 0.086 -3.888 10.109 1.00 0.00 H
ATOM 33 HA LEU Z 3 -2.475 -3.661 8.568 1.00 0.00 H
ATOM 34 HB2 LEU Z 3 -1.284 -1.469 8.843 1.00 0.00 H
ATOM 35 HB3 LEU Z 3 0.111 -2.162 8.026 1.00 0.00 H
ATOM 36 HG LEU Z 3 -2.606 -1.798 6.737 1.00 0.00 H
ATOM 37 HD11 LEU Z 3 -1.623 0.359 7.423 1.00 0.00 H
ATOM 38 HD12 LEU Z 3 -1.691 0.173 5.654 1.00 0.00 H
ATOM 39 HD13 LEU Z 3 -0.147 -0.043 6.513 1.00 0.00 H
ATOM 40 HD21 LEU Z 3 -1.168 -3.475 5.643 1.00 0.00 H
ATOM 41 HD22 LEU Z 3 -1.429 -2.035 4.630 1.00 0.00 H
ATOM 42 HD23 LEU Z 3 0.115 -2.250 5.489 1.00 0.00 H
ATOM 43 N VAL Z 4 -1.635 -5.424 7.029 1.00 3.17 N
ATOM 44 CA VAL Z 4 -1.165 -6.460 6.119 1.00 3.61 C
ATOM 45 C VAL Z 4 -1.791 -6.230 4.755 1.00 5.31 C
ATOM 46 O VAL Z 4 -3.014 -6.209 4.620 1.00 7.31 O
ATOM 47 CB VAL Z 4 -1.567 -7.872 6.593 1.00 5.31 C
ATOM 48 CG1 VAL Z 4 -1.012 -8.934 5.633 1.00 6.73 C
ATOM 49 CG2 VAL Z 4 -1.083 -8.120 8.018 1.00 5.48 C
ATOM 50 H VAL Z 4 -2.628 -5.282 7.146 1.00 0.00 H
ATOM 51 HA VAL Z 4 -0.080 -6.402 6.034 1.00 0.00 H
ATOM 52 HB VAL Z 4 -2.655 -7.939 6.585 1.00 0.00 H
ATOM 53 HG11 VAL Z 4 -1.303 -9.926 5.980 1.00 0.00 H
ATOM 54 HG12 VAL Z 4 -1.414 -8.766 4.634 1.00 0.00 H
ATOM 55 HG13 VAL Z 4 0.075 -8.864 5.603 1.00 0.00 H
ATOM 56 HG21 VAL Z 4 -1.377 -9.121 8.333 1.00 0.00 H
ATOM 57 HG22 VAL Z 4 0.003 -8.032 8.053 1.00 0.00 H
ATOM 58 HG23 VAL Z 4 -1.529 -7.383 8.686 1.00 0.00 H
ATOM 59 N SER Z 5 -0.966 -6.052 3.736 1.00 7.53 N
ATOM 60 CA SER Z 5 -1.526 -5.888 2.407 1.00 11.48 C
ATOM 61 C SER Z 5 -1.207 -7.085 1.529 1.00 16.35 C
ATOM 62 O SER Z 5 -0.437 -7.976 1.902 1.00 14.00 O
ATOM 63 CB SER Z 5 -1.031 -4.596 1.767 1.00 13.36 C
ATOM 64 OG SER Z 5 0.361 -4.652 1.540 1.00 15.80 O
ATOM 65 OXT SER Z 5 -1.737 -7.178 0.429 1.00 17.09 O
ATOM 66 H SER Z 5 0.033 -6.031 3.880 1.00 0.00 H
ATOM 67 HA SER Z 5 -2.610 -5.822 2.504 1.00 0.00 H
ATOM 68 HB2 SER Z 5 -1.543 -4.449 0.816 1.00 0.00 H
ATOM 69 HB3 SER Z 5 -1.254 -3.759 2.428 1.00 0.00 H
ATOM 70 HG SER Z 5 0.653 -3.831 1.137 1.00 0.00 H
TER 71 SER Z 5
HETATM 72 O HOH Z 101 0.935 -5.175 16.502 1.00 18.83 O
HETATM 73 H1 HOH Z 101 0.794 -5.522 15.621 1.00 0.00 H
HETATM 74 H2 HOH Z 101 1.669 -4.561 16.489 1.00 0.00 H
HETATM 75 O HOH Z 102 0.691 -8.408 17.879 1.00 56.55 O
HETATM 76 H1 HOH Z 102 1.392 -8.125 18.466 1.00 0.00 H
HETATM 77 H2 HOH Z 102 0.993 -8.356 16.972 1.00 0.00 H
CONECT 73 72
CONECT 74 72
CONECT 72 73 74
CONECT 76 75
CONECT 77 75
CONECT 75 76 77
END
Vasp’s POSCAR/CONTCAR Input¶
For periodic input Vasp’s POSCAR / CONTCAR input files are supported, for more information on the format visit the vasp-wiki.
For a molecular crystal of ammonia the input would look like:
H N
1.0000000000000000
5.0133599999999996 0.0000000000000000 0.0000000000000000
0.0000000000000000 5.0133599999999996 0.0000000000000000
0.0000000000000000 0.0000000000000000 5.0133599999999996
12 4
Cartesian
2.1985588943999996 1.7639005823999998 0.8801454815999999
1.7639005823999998 0.8801454815999999 2.1985588943999996
0.8801454815999999 2.1985588943999996 1.7639005823999998
4.8411510839999998 1.6194155471999998 4.9398140088000000
4.3563090384000001 2.4998116967999997 3.6324801215999996
3.5195792543999995 1.1535741359999998 4.0840334567999994
4.0840334567999994 3.5195792543999995 1.1535741359999998
4.9398140088000000 4.8411510839999998 1.6194155471999998
3.6324801215999996 4.3563090384000001 2.4998116967999997
2.4998116967999997 3.6324801215999996 4.3563090384000001
1.1535741359999998 4.0840334567999994 3.5195792543999995
1.6194155471999998 4.9398140088000000 4.8411510839999998
1.3746131783999997 1.3746131783999997 1.3746131783999997
3.9981545999999994 1.9910559239999999 4.4636450759999997
4.4636450759999997 3.9981545999999994 1.9910559239999999
1.9910559239999999 4.4636450759999997 3.9981545999999994
genFormat Input¶
The DFTB+ genFormat is supported for molecular and 3D periodic systems.
A valid input file for a molecular system is given here:
9 C
C Br H O
1 1 -8.9147060000E-02 -6.6786080000E-02 -1.0432907000E-01
2 2 1.7639746700E+00 2.6771621000E-01 4.2178865000E-01
3 3 -2.6325805000E-01 -1.1300550700E+00 -1.3052621000E-01
4 3 -7.4963702000E-01 3.9302570000E-01 6.1238499000E-01
5 3 -2.6130022000E-01 3.5462634000E-01 -1.0812232600E+00
6 4 4.7684499800E+00 7.6734388000E-01 1.2078966200E+00
7 1 5.5165496700E+00 2.5437564000E-01 4.3331738000E-01
8 3 6.6378745000E+00 3.1585526000E-01 5.3760272000E-01
9 3 5.1708208600E+00 -3.3263252000E-01 -4.6451965000E-01
For a periodic system the input would look like
2 F
Ga As
1 1 0.00 0.00 0.00
2 2 0.25 0.25 0.25
0.0000000E+00 0.0000000E+00 0.0000000E+00
0.2713546E+01 0.2713546E+01 0.0000000E+00
0.0000000E+00 0.2713546E+01 0.2713546E+01
0.2713546E+01 0.0000000E+00 0.2713546E+01
Gaussian External Input¶
The Gaussian external format is supported to use xtb with the Gaussian
program. A thin wrapper around the xtb binary is required to convert the
external call to a valid xtb program call.
An example input file is given here:
4 1 0 1
7 0.000000000000 0.000000000000 -0.114091591161 0.000000000000
1 -1.817280998039 0.000000000000 0.528409372569 0.000000000000
1 0.908640499019 -1.573811509290 0.528409372569 0.000000000000
1 0.908640499019 1.573811509290 0.528409372569 0.000000000000
Custom Annotations in Geometries¶
The element type is detected by the element symbol, xtb filters the input
string in the respective format for letters and uses them to figure out the
element type in a case-insensitive way.
While reading the geometry input the actual element symbol will be preserved
and not normalized, a buffer of four characters is available to hold the symbol
which will be used when referring to the element and printing the final geometry.
Note
Prior to version 6.3 only a two character buffer was available.
This allows to add annotations to the geometry input which will not affect the calculation, but show up in the output, log files and the final geometry printout. Consider the following xyz example:
24
13C 1.07317 0.04885 -0.07573
N 2.51365 0.01256 -0.07580
C* 3.35199 1.09592 -0.07533
N 4.61898 0.73028 -0.07549
C 4.57907 -0.63144 -0.07531
C 3.30131 -1.10256 -0.07524
C 2.98068 -2.48687 -0.07377
O(1) 1.82530 -2.90038 -0.07577
N 4.11440 -3.30433 -0.06936
C 5.45174 -2.85618 -0.07235
O 6.38934 -3.65965 -0.07232
N 5.66240 -1.47682 -0.07487
C 7.00947 -0.93648 -0.07524
C 3.92063 -4.74093 -0.06158
H 0.73398 1.08786 -0.07503
D 0.71239 -0.45698 0.82335
D 0.71240 -0.45580 -0.97549
D 2.99301 2.11762 -0.07478
H 7.76531 -1.72634 -0.07591
2H 7.14864 -0.32182 0.81969
3H 7.14802 -0.32076 -0.96953
H 2.86501 -5.02316 -0.05833
H 4.40233 -5.15920 0.82837
H 4.40017 -5.16929 -0.94780
Which is a valid input for xtb. Note that D and T can be used as synonyms
for hydrogen (H).
Note
Mangled names are not supported with crest and must be normalized.
Detailed Input¶
The xcontrol instruction set is inspired by the Turbomole control
file syntax. I decided to call it xcontrol instructions back than,
but here we will just call it (detailed) input for convenience.
The man page can be found here.
Note
The parser implemented is more general and limited by arbitrary choice to this syntax. At some point more common formats like JSON, YAML or XML might become available as alternative input formats.
To read an input file called xtb.inp use
> xtb --input xtb.inp coord
In the detailed input you have control about almost very global variable in the program, some instructions even check your input, but most of the time you should know what you are doing. Developed as a feature for developers, this is incredible powerful and naturally way to complicated for the average application. So in most cases you can safely rely on the internal defaults or the shipped global configuration file (should usually be the same).
I will walk you through some selected instructions you might find useful for your application.
Contents
Fixing, Constraining and Confining¶
In xtb different concepts of constraints are implemented,
so you should know which tool is best for you problem before you
start writing the detailed input.
We will go through this sections using the caffeine molecule
24
C 1.07317 0.04885 -0.07573
N 2.51365 0.01256 -0.07580
C 3.35199 1.09592 -0.07533
N 4.61898 0.73028 -0.07549
C 4.57907 -0.63144 -0.07531
C 3.30131 -1.10256 -0.07524
C 2.98068 -2.48687 -0.07377
O 1.82530 -2.90038 -0.07577
N 4.11440 -3.30433 -0.06936
C 5.45174 -2.85618 -0.07235
O 6.38934 -3.65965 -0.07232
N 5.66240 -1.47682 -0.07487
C 7.00947 -0.93648 -0.07524
C 3.92063 -4.74093 -0.06158
H 0.73398 1.08786 -0.07503
H 0.71239 -0.45698 0.82335
H 0.71240 -0.45580 -0.97549
H 2.99301 2.11762 -0.07478
H 7.76531 -1.72634 -0.07591
H 7.14864 -0.32182 0.81969
H 7.14802 -0.32076 -0.96953
H 2.86501 -5.02316 -0.05833
H 4.40233 -5.15920 0.82837
H 4.40017 -5.16929 -0.94780
Exact Fixing¶
In the exact fixing approach the Cartesian position of the selected atom is fixed in space by setting its gradient to zero and the degrees of freedom are removed from the optimization procedure and therefore the atoms stay in place in geometry optimizations.
For dynamics this exact fixing is automatically deactivated, since it usually leads to instabilities in the simulation.
To activate the exact fixing for atoms 1–10 and atom 12 as well as for all oxygen atoms, add
$fix
atoms: 1-10,12
elements: O
$end
to your detailed input, the atoms keyword refers to the numbering of the individual atoms in your input geometry. With this input the verbose output will show a short summary of the fixed atoms:
-------------------------------------------------
| Fixed Atoms |
-------------------------------------------------
* 13 fixed atom positions, i.e. in gradient
# Z position/Å
1 6 C 1.0731700 0.0488500 -0.0757300
2 7 N 2.5136500 0.0125600 -0.0758000
3 6 C 3.3519900 1.0959200 -0.0753300
4 7 N 4.6189800 0.7302800 -0.0754900
5 6 C 4.5790700 -0.6314400 -0.0753100
6 6 C 3.3013100 -1.1025600 -0.0752400
7 6 C 2.9806800 -2.4868700 -0.0737700
8 8 O 1.8253000 -2.9003800 -0.0757700
9 7 N 4.1144000 -3.3043300 -0.0693600
10 6 C 5.4517400 -2.8561800 -0.0723500
12 7 N 5.6624000 -1.4768200 -0.0748700
8 8 O 1.8253000 -2.9003800 -0.0757700
11 8 O 6.3893400 -3.6596500 -0.0723200
Note
Since version 6.3 the input is sorted and duplicates are removed automatically.
Constraining Potentials¶
Almost absolute control about anything in your system is archived
by applying constraining potentials. First of all the constraining
potentials offer a weaker version of the exact fixing, which is
invoked by the same syntax in the $constrain data group as
$constrain
atoms: 11
elements: C,N,8
$end
the program will not attempt to hold the Cartesian positions constant, but the distances between all selected atoms, here number 11 and all carbon, nitrogen and oxygen. For each atom pair a harmonic potential is generated to hold the distances at roughly the starting value, this even works without problems in dynamics.
For your caffeine molecule this results in a problem, which can easily be spotted in the verbose output of the constraints summary.
-------------------------------------------------
| Constraints |
-------------------------------------------------
* 15 constrained atom positions
positions referring to input geometry
# Z position/Å displ./Å
11 8 O 6.3577347 -3.6327225 -0.0684681 0.0000000
1 6 C 1.0687445 0.0520162 -0.0755782 0.0000000
3 6 C 3.3535252 1.0744217 -0.0774722 0.0000000
5 6 C 4.5969189 -0.6303196 -0.0745855 0.0000000
6 6 C 3.2896462 -1.0950551 -0.0735452 0.0000000
7 6 C 2.9629004 -2.4886091 -0.0702591 0.0000000
10 6 C 5.4425717 -2.8389078 -0.0699228 0.0000000
13 6 C 7.0086271 -0.9538835 -0.0749134 0.0000000
14 6 C 3.9536622 -4.7147069 -0.0641970 0.0000000
2 7 N 2.5030143 0.0336686 -0.0754494 0.0000000
4 7 N 4.6213728 0.7205067 -0.0770658 0.0000000
9 7 N 4.1215924 -3.2704219 -0.0683024 0.0000000
12 7 N 5.6601563 -1.4769082 -0.0732293 0.0000000
8 8 O 1.8493654 -2.9780046 -0.0690630 0.0000000
11 8 O 6.3577347 -3.6327225 -0.0684681 0.0000000
applying 105 atom pairwise harmonic potentials
applied force constant per pair: 0.0035714
effective force constant per atom: 0.0500000
constraining energy/grad norm: 0.0000000 0.0000000
Note
Since version 6.3 the input is sorted and duplicates are removed automatically.
Note that in some versions of xtb this leads to NaN for the
gradient, therefore double-check the constrained atom list for duplicates.
To constrain the atoms more tightly the force constant can be adjusted
$constrain
force constant=1.0
$end
this variable goes directly into the constraining procedure and is given in atomic unites (Hartree/Bohr²), for very high force constants this becomes equivalent to the exact fixing. Note the difference in the syntax as you are required to use an equal-sign instead of a colon, as you are modifying a global variable.
It is also possible to constrain selected internal coordinates, possible are distances, angles and dihedral angles as done here
$constrain
distance: 1, 2, 1.4
angle: 5, 7, 8, auto
dihedral: 3, 4, 1, 7, 180
$end
Note
This printout is not yet fully integrated in the released versions and
might not work as expected.
For the experimental constraining potentials supporting this features
use the all-caps keyword variants (DISTANCE, ANGLE and DIHEDRAL).
Note that those are not available for the scan feature.
Distance constraints are given in Ångström, while angle constraints are given
in degrees.
The distances are defined by two atom number referring to the order in
your coordinate input, angles are defined by three atom numbers and
dihedral angles by four atoms, in any case the atoms do not have to
be connected by bonds. The last argument is always the value which should
be used in the constraining potential as reference, if you decide to
use the current value auto can be passed. The constraints will be
printed to the screen (the newer implementation may require the verbose mode,
to trigger the printout of the constraint summary), we check this setup
for the caffeine molecule
-------------------------------------------------
| Constraints |
-------------------------------------------------
* 1 constrained distance
# Z # Z value/Å actual/Å
1 6 C 2 7 N 1.4000000 1.4409371
constraining potential exponent: 2.0000000
applied force constant per dist.: 0.0500000
effective force constant per atom: 0.0250000
constraining energy/grad norm: 0.0002992 0.0109403
* 1 constrained angle
# Z # Z # Z value/° actual/°
5 6 C 7 6 C 8 8 O 150.4357763 150.4357763
applied force constant per angle: 0.0500000
effective force constant per atom: 0.0166667
constraining energy/grad norm: 0.0000000 0.0000000
* 1 constrained dihedral angle
# Z # Z # Z # Z value/° actual/°
3 6 C 4 7 N 1 6 C 7 6 C 180.0000000 -179.9396548
applied force constant per angle: 0.0500000
effective force constant per atom: 0.0125000
constraining energy/grad norm: 0.0000000 0.0000629
total constraint energy/grad norm: 0.0002993 0.0110032
You can find the constraint energy and gradient at the end of the summary, check for unphysical high values of the energy and gradient here to verify your constraint setup otherwise you might encounter strange behaviour in the following optimization or dynamics to adhere this constraints.
If you are not quite sure which distances or angles you want to constrain, run
> cat geosum.inp
$write
distances=true
angles=true
torsions=true
$end
> xtb --define --verbose --input geosum.inp caffeine.xyz
and have a look at the geometry summary for your molecule. The $write
data group toggles the printout in the property section and also some
printouts in the input section.
For caffeine the geometry summary including only the distances looks like this
-------------------------------------------------
| Geometry Summary |
-------------------------------------------------
molecular mass/u : 194.1926000
center of mass at/Å : 4.0569420 -1.6298957 -0.0733327
moments of inertia/u·Å² : 4.7317175E+02 7.1109348E+02 1.1745947E+03
rotational constants/cm⁻¹ : 3.5626878E-02 2.3706633E-02 1.4351872E-02
* 25 selected distances
# Z # Z value/Å
1 6 C 2 7 N 1.4409371
2 7 N 3 6 C 1.3698478
3 6 C 4 7 N 1.3186949
4 7 N 5 6 C 1.3623047
2 7 N 6 6 C 1.3652477
5 6 C 6 6 C 1.3618461
6 6 C 7 6 C 1.4209574
7 6 C 8 8 O 1.2271501
7 6 C 9 7 N 1.3977057
9 7 N 10 6 C 1.4104346
10 6 C 11 8 O 1.2347703
5 6 C 12 7 N 1.3741439
10 6 C 12 7 N 1.3953559
12 7 N 13 6 C 1.4514011 (max)
9 7 N 14 6 C 1.4496299
1 6 C 15 1 H 1.0929740
1 6 C 16 1 H 1.0928728
1 6 C 17 1 H 1.0928837
3 6 C 18 1 H 1.0829302 (min)
13 6 C 19 1 H 1.0932399
13 6 C 20 1 H 1.0945661
13 6 C 21 1 H 1.0945601
14 6 C 22 1 H 1.0927021
14 6 C 23 1 H 1.0949866
14 6 C 24 1 H 1.0949141
* 4 distinct bonds (by element types)
Z Z # av. dist./Å max./Å min./Å
1 H 6 C 10 1.0926630 1.0949866 1.0829302
6 C 6 C 2 1.3914017 1.4209574 1.3618461
6 C 7 N 11 1.3941548 1.4514011 1.3186949
6 C 8 O 2 1.2309602 1.2347703 1.2271501
There is no electronic structure information used at this point but a simple geometric model to select distances, which can get too few or too many bonds or angles in this printout.
Confining in a Cavity¶
If you are running dynamics for systems that are non-covalently bound, you may encounter dissociation in the dynamics. If you want to study the bound complex, you can try to confine the simulation in a little sphere, which keeps the molecules from escaping. The detailed input looks like
$wall
potential=logfermi
sphere: auto, all
$end
You can be more precise on the radius by giving the value in Bohr instead
of auto. The automatically determined radius is based on the largest
interatomic distance in the structure plus some offset.
The logfermi potential is best suited for confinements, but not yet the
default potential.
When using this input with the caffeine molecule the automatically determined radius is about 5.6 Å, which should be large enough to contain a molecule of its size. At first it might be surprising to find that the confining energy is about +84 kcal/mol, but we did we did not account for the placement of the molecule, relative to the center of potential within our chosen input. Currently, the center point of the spherical logfermi potential is set at the origin (0,0,0) and the center of mass of the caffeine molecule is about 4.4 Å away from it, so our molecule is stuck halfway in the wall we just created.
The sphere used to construct the potential is represented by the transparent teal dots placed on a fine Lebedev grid. Visual inspection suggests that the potential is misplaced.¶
To cope with this we should put the center of mass of the caffeine molecule
at the origin, this can be done by adding the $cma instruction to the input
file, which shifts the coordinates with the center of mass and aligns
the molecule to its principal axes of inertia.
The caffeine molecule is now shifted correctly inside the potential. The confining energy, for the correctly placed potential is now 0 kcal/mol.¶
Note
The center point for all wall potentials is always placed at the origin, which cannot be changed with the currently available input options. Therefore, we resort to modifying our input coordinates here.
Different Potential Shapes¶
Currently two different potential shapes are implemented and can be
selected with the potential instruction.
The logfermi potential shape is given by the expression
where
kB is the Boltzmann constant,
T is formally the temperature but can be used to scale
the strength of the potential (adjustable by temp=<real>, within the $wall group),
β is the steepness of the potential (adjustable by beta=<real>),
RA are the cartesian coordinates of atom A,
O is the origin (0,0,0) and
Rsphere is the radius of the sphere used for confining.
The default potential shape is a simple polynomial to the power α
(adjustable by alpha=<int>).
The formula that is evaluated in the program is
The main (dis)advantage of this shape is that the radius of the sphere
is a relative quantity compared to the size of the molecule.
The auto generator of the sphere radius takes this into account,
by rescaling the largest distance in the molecule instead of adding
a constant shift.
A clear disadvantage of this potential shape it that the gradient does
not vanish inside the sphere and can compress a molecule artificially.
Available potential shapes with energy and gradient contribution.¶
Anisotropic Potentials¶
For some molecules an isotropic spherical cavity is not suitable for confinement, since the molecule might have a rod-like or oblate shape. Instead of sphere we can use an ellipsoid to construct an anisotropic cavity, there is no limitation for the potential shape since we use a simple rescaling to introduce anisotropy.
The input file for an anisotropic potential would look like
$wall
potential=logfermi
ellipsoid: 13.5,11.1,8.6,all # values in Bohr
$end
As for the isotropic one can use the auto keyword to replace any of the
the three radii with an automatically determined value.
The automatic determined value is the automatic isotropic sphere radius,
so letting all three values be autodetermined results in an isotropic potential.
As before, we have to deal with the issue that the center of mass of our caffeine molecule and the origin do not coincident, this time we use a Python interpreter with ASE support for this job
from ase.io import read, write
mol = read('caffeine.xyz')
mol.set_positions(mol.get_positions() - mol.get_center_of_mass())
write('caffeine_shifted.xyz', mol)
Finally we can check xtb with the new coordinates and the above input file and
we find that the confining energy is zero in the initial geometry.
Shifted caffeine molecule in an anisotropic potential, note that the structure is not rotated this time.¶
Using Multiple Potentials¶
Since version 6.0 an arbitrary number of wall potentials is supported.
Similar to the constraint keywords one could create multiple wall potentials
by repeating sphere and/or ellipsoid instructions like
$wall
potential=logfermi
sphere: auto, all
ellipsoid: 13.5,11.1,8.6,all # values in Bohr
$end
This could be used to confine different fragments in different sized spheres. The only restriction is that the potential shape is global.
Absolute Control¶
As I promised you can control almost everything, the xcontrol(7) man page
is a good starting point to get acquainted with the detailed input. This
poses the usual hindrance of actually reading the documentation
(since you are here, you are already above average, thumbs up).
A practical alternative is to just dump the complete internal settings of the program to an input file and start playing around with it. To do so, run
> xtb --input default.inp --define --copy coord
The file default.inp has not to be present when starting the program
in --copy mode, since the default.inp will be generated for you.
The --define flags makes sure that the program only checks your setup
and does not perform any calculation on the input coordinates.
Have a look at the first lines of default.inp:
$cmd xtb --input default.inp --define --copy coord
$date 2019/03/05 at 08:50:26.651
$chrg 0
$spin 0
...
This is actually the command you used in the first place to invoke the
program, next you find the timestamp when the program was started and
then system specific information about charge and spinstate of your system,
this is what I understand as a self-documenting program run.
$cmd and $date are cosmetic features and will never influence
any calculation if included in the detailed input, but I figured that
they might become handy if you look back into your calculations when
putting together the manuscript or taking over a project from your,
now graduated, fellow coworker.
The rest of the file represent every accessible variable documented
in the xcontrol(7) man page with its current setting, this should be
quite a lot. So lets focus say on the $wall group:
...
$wall
potential=polynomial
alpha=30
beta=6.000000000000000
temp=300.0000000000000
autoscale=1.000000000000000
axisshift=3.500000000000000
...
The default potential is a polynomial one, you want to change this to
the logfermi potential. alpha is only needed for the polynomial
potential, we use beta and temp in our potential.
The steepness of our potential can be adjusted by modifying the value
of beta, since our potential is multiplied with the thermal energy
we can scale it by increasing it temperature in temp.
autoscale is a factor the automatic determined sphere axes are
multiplied with, a default of 1.0 seems reasonable here, but sometimes
we need more space or want to squeeze everything a bit together.
We can also adjust the constant shift value used in the generation
of the automatic axes, but on a second thought this value might be
just fine, so we do not modify axisshift today.
This is an awful lot of information in a small block and quite essential
for your calculation using a confining potential, all details on this
can be found in xcontrol(7) man page at the group instruction
of interest.
Tip
If you are happy with all this setting you can just use this file as
your .xtbrc and place it somewhere in your XTBPATH.
Global Configuration File¶
The global configuration file called .xtbrc has to be around somewhere
in your XTBPATH so xtb is able to find it and uses the very same
syntax as the detailed input. Every instruction (key=value) you can
use in your detailed input file can be present in your global configuration
file. System specific instructions (key: value) will not work, of course.
To check which .xtbrc is read, start the program in verbose mode and
check the Calculation Setup section in the output.
Rules for Control¶
This section is intended to briefly explain the currently applied rules to parse the detailed input file.
Every instruction is started by a flag ($) and terminated by the next flag.
An instruction is only valid if the flag is in the first letter, the
instruction name is the rest of the register (line).
A valid instruction opens its block with its own options, every option
is a key-value pair. Invalid instructions are ignored without further warning.
There are two kind of instructions, logical and groups. Logical instructions toggle a specific operation and cannot contain a option block while group instructions only open the option block without any further actions.
Groups with the same name can occur multiple times and are merged before parsing.
There are two kind of options, key=value pairs set global variables and
can only be used once, they are locked at the first encounter of the key,
regardless of the value, in case an invalid value is given the default is used
as fallback and cannot be modified by subsequent options with the same key.
Options of the kind key: values,... can be present multiple times and
are handled differently depending on the context they are used in.
For example the atoms: instruction usually appends atoms to an list,
while distance: in $constrain applies a quadratic potential to
the atom pair specified.
Compiling from Source¶
This guide is intended to help developers to get our programs running.
Note
To install our programs refer to Setup and Installation. If you come here from Setup and Installation, since our instructions have not worked for you, why not drop us a hint at the issue tracker?
The xtb source code is hosted at GitHub.
Contents
Building with meson¶
The xtb program source comes with a meson build-system
(see mesonbuild.com for details).
Despite being a rather young build-system, we decided to commit to the
idea of using it for xtb due to its simplicity and speed compared
to competing build-systems like Scons or Make.
To build xtb from the source the meson build system can be used.
For a decent Fortran support verson 0.51 of meson or newer is required,
additionally the default backend ninja is required with version 1.7 or newer.
Getting meson¶
To install the meson build system first check your package manager for an up-to-date meson version,
usually this will also install ninja as dependency.
Alternatively you can install the latest version of meson and ninja with pip (or pip3 depending on your system):
pip install meson ninja [--user]
If you prefer conda as a package manage you can install meson and ninja from the conda-forge channel.
Make sure to select the conda-forge channel for searching packages.
conda config --add channels conda-forge
conda install meson ninja
Configure Intel Fortran build with MKL¶
The recommended build for xtb is with Intel Parallel Studio using the Intel Fortran compiler and the Math Kernel Library as default backend.
Precompiled, statically linked xtb binaries for Linux are provided at the release page.
The setup for the linear algebra backend defaults to MKL, therefore, only the compilers have to exported before configuring the build:
export FC=ifort CC=icc
meson setup build --buildtype=release
After the configuration step the build can be performed with ninja:
ninja -C build
Note, ninja will by default use all the threads available on your system.
Note
If you share the build machine with others it might be helpful to reduce the number of concurrent jobs using the -j flag.
By default the binary will be linked statically, other supported backends are:
backend |
linked against |
|---|---|
mkl-static |
static MKL (default) |
mkl |
shared MKL |
mkl-rt |
MKL real time library |
openblas |
OpenBLAS and if required LAPACK |
netlib |
BLAS and LAPACK |
custom |
|
Note
If you are using the MKL provided by conda-forge you have to link against the netlib backend
Configure GCC build with OpenBLAS¶
xtb can also be compiled with GCC version 8 or later.
For this example we additonally choose to change the linear algebra backend to OpenBLAS, if you have Intel Parallel Studio installed, you can leave out the last argument to get the MKL backend.
export FC=gfortran CC=gcc
meson setup build --buildtype=release -Dla_backend=openblas
The build system will check if the OpenBLAS library provides LAPACK features as well, if this is not the case it will additionally search for LAPACK.
If you are compiling xtb on Darwin platforms, ensure that GCC is the actual GCC and not clang.
The build can be performed just like before:
ninja -C build
Testing the build with meson¶
After successfully building the xtb program ensure that it is working as expected. Run the testsuite with
ninja -C build test
All tests should pass, otherwise open an issue.
Installing with meson¶
To use xtb in production or to pack a release with precompiled binaries the project should be installed with ninja.
The installation prefix defaults to /usr/local on Linux systems, you might want to adjust this first by configuring your build with
meson configure build --prefix=$HOME/.local
To perform the actual installation run
ninja -C build install
Depending on the installation prefix and your user rights ninja might ask for the root access to perform the installation.
Building with GPU support¶
This projects can run on accelerator devices from NVIDIA. The compilation of the GPU version requires the NVIDIA HPC SDK, dupped NVHPC for brevity. The NVHPC compilers are available for free here.
Note
It is highly recommended to carefully compare the performance of the CPU version with the GPU version before starting production runs. Certain problem sizes can profit more from different accelerator devices than others.
To throw in some numbers as guidance for a single point calculation of a 3000 atom system with GFN2-xTB(ALPB) using xtb version 6.4.0:
Compiler |
Hardware |
Walltime |
|---|---|---|
Intel 18 |
4 cores @ Intel Xeon CPU E3-1270 v5 |
13 min |
Intel 18 |
8 cores @ Intel Xeon Gold 6148 CPU |
7 min |
NVHPC 20.7 |
Tesla K80 (cc35) |
7 min |
NVHPC 20.7 |
Tesla V100 (cc70) |
2 min |
The NVHPC provides TCL environment modules which are the preferred way to setup the compilers, if your module environment is already configured, you can just go ahead and
module load nvhpc
Note
The TCL environment modules are usually installed in the highest level of
your chosen install prefix, i.e. /opt/nvhpc/modulefiles if you
installed into /opt/nvhpc.
If you do not have a module environment available on your (local) system
you can install the TCL environment modules under Ubuntu with the
environment-module package or the newer Lua environment modules with
the lmod package.
With the NVHPC compilers available, configure a build with
export FC=nvfortran CC=nvc
meson setup build_gpu --prefix=$HOME/.local -Dla_backend=netlib -Dgpu=true -Dcusolver=true
You can select the correct compute capability of your device with -Dgpu_arch=70.
Note
Support for NVHPC in meson is available since version 0.56.0.
Compile and install the project with
ninja -C build_gpu install
If you used the provided TCL environment modules of the NVHPC, you can use xtb in a similar way by including the automatically generated TCL environment module in the install prefix with:
echo "prereq nvhpc" >> ~/.local/share/modules/modulefiles/xtb/*
module use ~/.local/share/modules/modulefiles
module load xtb
Now you have a working version of xtb which can make use of your GPU.
To check if your GPU is utilized correctly you can either track the GPU usage with
nvidia-smi command line tool or set PGI_ACC_NOTIFY=3 when running xtb
as environment variable to get information on which kernels are launched on which device.
If you have multiple accelerator devices attached to your system you can select them
at runtime with CUDA_VISIBLE_DEVICES=<int>.
Supported Compilers¶
This is a non-comprehensive list of tested compilers for xtb with the meson build system.
Compiler |
Version |
Platform |
Architecture |
|
|---|---|---|---|---|
GCC |
10.2 |
Ubuntu 20.04 |
x86_64 |
latest |
GCC |
10.2 |
Manjaro Linux |
x86_64 |
6.4.0 |
GCC |
10.2 |
Windows Server 2019 |
x86_64 |
6.4.0, latest |
GCC |
9.3 |
Ubuntu 18.04 |
x86_64 |
6.4.0 |
GCC |
9.3 |
Ubuntu 20.04 |
x86_64 |
latest |
GCC |
9.3 |
Centos 7 |
ppc64le, aarch64 |
6.4.0 |
GCC |
9.3 |
Centos 6 |
x86_64 |
6.4.0 |
GCC |
9.3 |
MacOS 10.15.7 |
x86_64 |
6.4.0, latest |
GCC |
8.4 |
Ubuntu 20.04 |
x86_64 |
latest |
GCC |
7.5 |
Ubuntu 18.04 |
x86_64 |
6.4.0 |
Intel |
2021.1 |
Ubuntu 20.04 |
x86_64 |
6.4.0, latest |
Intel |
18.0.2 |
OpenSuse 42.1 |
x86_64 |
6.4.0 |
NVHPC |
20.11, 21.1 |
Manjaro Linux |
x86_64 |
6.4.0 |
NVHPC |
20.9 |
Centos 8 |
x86_64 + cc70 |
6.4.0 |
NVHPC |
20.7 |
OpenSuse 42.1 |
x86_64 + cc35 |
6.4.0 |
The list was started with version 6.4.0 and will be continued for future released.
The latest version refers to the continuously tested compiler tool chains in the xtb repository.
For GPU enabled builds the compute-capability is given together with the architecture.
Note
First class compiler support in xtb comes only with continuous testing, if you
want to see a particular compiler, platform or architecture in the list above,
please reach out to us at the discussion board,
open an issue or submit
a continuous integration workflow with a pull request to xtb.
Singlepoint Calculations¶
Contents
Note
Generally, a singlepoint calculation will be carried out automatically before every other calculation done with xtb.
Input¶
To start a singlepoint calculation with xtb only a molecular geometry is needed. xtb supports the TURBOMOLE coordinates (.coord/.tmol), any valid Xmol (e.g. .xyz), mol files (.mol), Structure-Data files (.sdf), Protein Database Files (.pdb), Vasp’s POSCAR and CONTCAR files (.poscar/.contcar/.vasp) and DFTB+ genFormat files (.gen).
For a detailed overview over all geometry input formats see Geometry Input
Example TURBOMOLE input coordinates for H2O (e.g. coord):
$coord
0.00000000000000 0.00000000000000 -0.73578586109551 o
1.44183152868459 0.00000000000000 0.36789293054775 h
-1.44183152868459 0.00000000000000 0.36789293054775 h
$end
Example Xmol input coordinates for H2O (e.g. h2o.xyz):
3
Comment Line
O 0.0000000 0.0000000 -0.3893611
H 0.7629844 0.0000000 0.1946806
H -0.7629844 0.0000000 0.1946806
Example SDF input for H2O (e.g. h2o.sdf)
Water
xtb 11041909383D
Comment line
3 2 0 0 0 999 V2000
-0.2191 -0.3098 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
0.7400 -0.2909 -0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
-0.5210 0.6007 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
1 3 1 0 0 0 0
M END
> <Formula>
H2 O
> <Mw>
18.01528
> <SMILES>
O([H])[H]
> <CSID>
937
$$$$
Note
To use input coordinates in SDF format the .sdf suffix is required.
Charge and Multiplicity¶
By default xtb will search for .CHRG and .UHF files which contain the molecular charge
and the number of unpaired electrons as an integer, respectively.
Example .CHRG file for a molecule with a molecular charge of +1:
> cat .CHRG
1
Example .CHRG file for a molecule with a molecular charge of -2:
> cat .CHRG
-2
Example .UHF file for a molecule with two unpaired electrons:
> cat .UHF
2
The molecular charge can also be specified directly from the command line:
> xtb coord --chrg <INTEGER>
which is equivalent to
> echo <INTEGER> > .CHRG && xtb coord
This also works for the unpaired electrons as in
> xtb coord --uhf <INTEGER>
being equivalent to
> echo <INTEGER> > .UHF && xtb molecule.xyz
Example for a +1 charged molecule with 2 unpaired electrons:
> xtb --chrg 1 --uhf 2
Note
The molecular charge or number of unpaired electrons specified from the command line will override specifications provided by .CHRG, .UHF and the xcontrol input!
The imported specifications are documented in the output file in the Calculation Setup section.
-------------------------------------------------
| Calculation Setup |
-------------------------------------------------
program call : xtb molecule.xyz
hostname : user
coordinate file : molecule.xyz
omp threads : 4
number of atoms : 3
number of electrons : 7
charge : 1 # Specified molecular charge
spin : 1.0 # Total spin from number of unpaired electrons (S=2*0.5=1)
first test random number : 0.54680533077496
Note
Note that the position of the input coordinates is totally unaffected
by any command-line arguments, if you are not sure, whether xtb tries
to interpret your filename as flag use -- to stop the parsing
as command-line options for all following arguments.
> xtb -- -oh.xyz
To select the parametrization of the xTB method you can currently choose from four different geometry, frequency and non-covalent interactions (GFN) parametrizations/methods, which differ mostly in the cost–accuracy ratio,
> xtb --gfn 0 coord
> xtb --gfn 1 coord
> xtb --gfn 2 coord
> xtb --gfnff coord
GFN2-xTB is the default parametrization. Also available are GFN1-xTB, GFN0-xTB (Notice: separate parameter file necessary!) as well as the GFN-FF force-field.
Accuracy and Iterations¶
Accuracy¶
The accuracy of the xTB calculation can be adjusted by the commandline option
--acc. The accuracy determines the integral screening thresholds and the
SCC convergence criteria and can be adjusted continuous in a range from
0.0001 to 1000, where tighter criteria are set for lower values of accuracy.
To change the calculation accuracy call xtb with
> xtb coord --acc <REAL>
By default the accuracy multiplier is set to 1, for a few accuracy settings the resulting numerical thresholds are shown below:
Accuracy |
30 |
1 |
0.2 |
|---|---|---|---|
Integral cutoff |
20.0 |
25.0 |
32.0 |
Integral neglect |
3.0 · 10⁻⁷ |
1.0 · 10⁻⁸ |
2.0 · 10⁻⁹ |
SCC convergence / Eh |
3.0 · 10⁻⁵ |
1.0 · 10⁻⁶ |
2.0 · 10⁻⁷ |
Wavefunction convergence / e |
3.0 · 10⁻³ |
1.0 · 10⁻⁴ |
2.0 · 10⁻⁵ |
Note
The wavefunction convergence in GFN2-xTB is chosen automatically a bit tighter than for GFN1-xTB.
Iterations¶
The number of iterations allowed for the SCC calculation can be adjusted from the command line:
> xtb coord --iterations <INTEGER>
The default number of iterations in the SCC is set to 250.
Fermi-smearing¶
The electronic temperature \(T_{el}\) is used as an adjustable parameter, employing so-called Fermi smearing to achieve fractional occupations for systems with almost degenerate orbital levels. This is mainly used to take static correlation into account or to e.g. investigate thermally forbidden reaction pathways.
\(T_{el}\) enters the GFNn-xTB Hamiltonian as
and the orbital occupations for a spin orbital \(\psi_{i}\) are given by
The default electronic temperature is \(T_{el}\) = 300 K.
\(T_{el}\) can be adjusted by the command line:
> xtb --etemp <REAL> molecule.xyz
The specified electronic temperature is documented in the output file in the Self-Consistent Charge Iterations section
-------------------------------------------------
| Self-Consistent Charge Iterations |
-------------------------------------------------
...................................................
: SETUP :
:.................................................:
: # basis functions 12 :
: # atomic orbitals 12 :
: # shells 8 :
: # electrons 16 :
: max. iterations 250 :
: Hamiltonian GFN2-xTB :
: restarted? false :
: GBSA solvation false :
: PC potential false :
: electronic temp. 5000.0000000 K :
: accuracy 1.0000000 :
: -> integral cutoff 0.2500000E+02 :
: -> integral neglect 0.1000000E-07 :
: -> SCF convergence 0.1000000E-05 Eh :
: -> wf. convergence 0.1000000E-03 e :
: Broyden damping 0.4000000 :
...................................................
Note
Sometimes you may face difficulties converging the self consistent charge iterations. In this case increasing the electronic temperature and restarting at the converged calculation with normal temperature can help.
> xtb coord --etemp 1000.0 && xtb coord --restart
Vertical Ionization Potentials and Electron Affinities¶
xtb can be used to calculate vertical ionization potentials (IP) and electron affinities (EA) applying
a specially reparameterized GFN1-xTB version. The special purpose parameters are documented in the .param_ipea.xtb
parameter file.
The vertical ionization potential or electron affinity is obtained as the energy difference between the corresponding molecule groundstate and its ionized species in the same geometry.
Note
The sign of the IP and EA can differ in the literature due to different definitions.
The vertical IP and EA calculations can be evoked from the command line either separately or combined.
> xtb coord --vip
> xtb coord --vea
> xtb coord --vipea
Note
It is recommended to optimize the molecule geometry prior to the vipea calculation.
> xtb coord --opt && xtb xtbopt.coord --vipea
The calculated IP and/or EA are then corrected empirically, both the empirical shift and the final IP and/or EA are documented in the output in the vertical delta SCC IP calculation and vertical delta SCC EA calculation sections.
Example output for the optimized Water molecule:
-------------------------------------------------
| vertical delta SCC IP calculation |
-------------------------------------------------
*** removed SETUP and SCC details for clarity ***
:::::::::::::::::::::::::::::::::::::::::::::::::::::
:: SUMMARY ::
:::::::::::::::::::::::::::::::::::::::::::::::::::::
:: total energy -5.141603209729 Eh ::
:: gradient norm 0.051348781702 Eh/α ::
:: HOMO-LUMO gap 6.668725933430 eV ::
::.................................................::
:: SCC energy -5.189558706232 Eh ::
:: -> electrostatic 0.159050410368 Eh ::
:: repulsion energy 0.048093066315 Eh ::
:: dispersion energy -0.000137569813 Eh ::
:: halogen bond corr. 0.000000000000 Eh ::
:: add. restraining 0.000000000000 Eh ::
:::::::::::::::::::::::::::::::::::::::::::::::::::::
------------------------------------------------------------------------
empirical IP shift (eV): 4.8455 # Empirical shift
delta SCC IP (eV): 13.7897 # Finally calculated vertical IP (Exp.: 12.6 eV)
------------------------------------------------------------------------
-------------------------------------------------
| vertical delta SCC EA calculation |
-------------------------------------------------
*** removed SETUP and SCC details for clarity ***
:::::::::::::::::::::::::::::::::::::::::::::::::::::
:: SUMMARY ::
:::::::::::::::::::::::::::::::::::::::::::::::::::::
:: total energy -5.929826433613 Eh ::
:: gradient norm 0.016238133270 Eh/α ::
:: HOMO-LUMO gap 7.760066297206 eV ::
::.................................................::
:: SCC energy -5.977781930116 Eh ::
:: -> electrostatic 0.169754616317 Eh ::
:: repulsion energy 0.048093066315 Eh ::
:: dispersion energy -0.000137569813 Eh ::
:: halogen bond corr. 0.000000000000 Eh ::
:: add. restraining 0.000000000000 Eh ::
:::::::::::::::::::::::::::::::::::::::::::::::::::::
------------------------------------------------------------------------
empirical EA shift (eV): 4.8455 # Empirical shift
delta SCC EA (eV): -2.0320 # Finally calculated vertical EA
------------------------------------------------------------------------
Global Electrophilicity Index¶
xtb can be used for direct calculation of Global Electrophilicity Indexes (GEI) that can be used to estimate the electrophilicity or Lewis acidity of various compounds from vertical IPs and EAs. In xtb the GEI is defined as:
The GEI calculation can be evoked from the command line:
> xtb coord --vomega
The calculated GEI is documented in the output after the vertical delta SCC EA calculation section
------------------------------------------------------------------------
Calculation of global electrophilicity index (IP+EA)²/(8·(IP-EA))
Global electrophilicity index (eV): 1.0923 #GEI for water
------------------------------------------------------------------------
Fukui Index¶
The Fukui indexes or condensed Fukui function can be calculated to estimate the most electrophilic or nucleophilic sites of a molecule.
The two finite representations of the Fukui function are defined as
representing the electrophilicity (susceptibility of an nucleophilic attack) of an atom in a molecule with N electrons and
representing the nucleophilicity (susceptibility of an electrophilic attack) of an atom.
The radical attack susceptibility is described by
Note
As the Fukui indexes depend on occupation numbers and population analysis (see Properties), they are sensitive toward basis set changes. Therefore Fukui indexes should not be recognized as absolute numbers but as relative parameters in the same system.
A Fukui index calculation can be evoked from the command line:
> xtb coord --vfukui
The calculated Fukui indexes are documented in the Fukui index Calculation section of the output.
Example: BF3¶
Fukui index Calculation
1 -15.6291014 -0.156291E+02 0.835E+00 13.96 0.0 T
2 -15.6761217 -0.470203E-01 0.533E+00 13.46 1.0 T
3 -15.6768113 -0.689578E-03 0.156E+00 13.00 1.0 T
4 -15.6769156 -0.104364E-03 0.175E-01 12.86 1.0 T
5 -15.6769184 -0.275858E-05 0.213E-02 12.90 2.3 T
6 -15.6769197 -0.132996E-05 0.325E-03 12.91 15.4 T
7 -15.6769197 0.872775E-08 0.253E-03 12.91 19.8 T
8 -15.6769197 -0.144533E-07 0.264E-05 12.91 1896.8 T
9 -15.6769197 -0.126121E-11 0.650E-06 12.91 7694.1 T
SCC iter. ... 0 min, 0.001 sec
gradient ... 0 min, 0.000 sec
1 -14.9103537 -0.149104E+02 0.313E+00 8.30 0.0 T
2 -14.9107747 -0.421013E-03 0.195E+00 8.21 1.0 T
3 -14.9108376 -0.628755E-04 0.217E-01 8.29 1.0 T
4 -14.9108954 -0.578357E-04 0.166E-01 8.21 1.0 T
5 -14.9003399 0.105555E-01 0.141E+00 8.21 1.0 T
6 -14.9108133 -0.104734E-01 0.172E-01 8.22 1.0 T
7 -14.9109267 -0.113342E-03 0.872E-02 8.22 1.0 T
8 -14.9109654 -0.387429E-04 0.200E-02 8.23 2.5 T
9 -14.9109672 -0.181816E-05 0.417E-03 8.24 12.0 T
10 -14.9109673 -0.412949E-07 0.111E-03 8.23 45.1 T
11 -14.9109673 -0.551257E-08 0.351E-04 8.23 142.6 T
12 -14.9109673 -0.493735E-09 0.682E-05 8.23 733.6 T
SCC iter. ... 0 min, 0.001 sec
gradient ... 0 min, 0.000 sec
# f(+) f(-) f(0) #Fukui indexes
1 B -0.300 0.005 -0.148
2 F -0.233 -0.335 -0.284
3 F -0.233 -0.335 -0.284
4 F -0.233 -0.335 -0.284
The Fukui indexes for BF3 indicate the most negative f(+) value and a positive value for f(-) at the boron atom. Thus, a nucleophilic attack can be expected at the boron atom.
Properties¶
In this chapter, all necessary information about the properties of xTB will be given. Description of how to acquire different output information will be provided. Calculation of FOD will be described.
Contents
General printout¶
First the orbital energies and occupation are printed, where the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) are marked. The HOMO-LUMO gap and the Fermi-level are summed up.
-------------------------------------------------
| Property Printout |
-------------------------------------------------
* Orbital Energies and Occupations
# Occupation Energy/Eh Energy/eV
-------------------------------------------------------------
1 2.0000 -0.6801050 -18.5066
2 2.0000 -0.5683264 -15.4649
3 2.0000 -0.5108650 -13.9013
4 2.0000 -0.4463919 -12.1469 (HOMO)
5 0.0826818 2.2499 (LUMO)
6 0.2518567 6.8534
-------------------------------------------------------------
HL-Gap 0.5290737 Eh 14.3968 eV
Fermi-level -0.1818551 Eh -4.9485 eV
The information provided by the printout can be modified and extended. This can be done either by using the option-flags when calling the program (Commandline Usage), or by editing the input file (Detailed Input). The kind of default information given is determined by the GFN-xTB version used. The default values called by the program are given:
- --pop
requests printout of Mulliken population analysis
- --molden
requests printout of molden file
- --dipole
requests printout of dipole moments
- --wbo
requests Wiberg bond order printout
GFN1-xTB¶
Default settings for GFN1-xTB first prints the Mulliken and CM5 charges. n(x) denotes the population partioned to the x = s/p/d shells:
Mulliken/CM5 charges n(s) n(p) n(d)
1 O 0.67569 0.33312 1.682 4.994 0.000
2 H -0.33784 -0.16656 0.662 0.000 0.000
3 H -0.33784 -0.16656 0.662 0.000 0.000
Wiberg bond orders describe the partial bond orders and their disposition onto the atoms:
Wiberg/Mayer (AO) data.
largest (>0.10) Wiberg bond orders for each atom
total WBO WBO to atom ...
1 O 1.782 H 2 0.891 H 3 0.891
2 H 0.892 O 1 0.891
3 H 0.892 O 1 0.891
The molecular dipole moment and its cartesian components calculated from the electron density. The components are given in atomic units while the total dipole moment is given in Debye, to convert from atomic units to Debye multiply by 2.5417 D/au.
dipole moment from electron density (au)
X Y Z
0.8659 0.0000 0.6123 total (Debye): 2.696
GFN2-xTB¶
Default settings for GFN2-xTB first prints populations and coefficients. From left to right, these are the atomic number Z, Coordination number CN, Atomic partial charge q, Dispersion coefficient C6, Polarizability alpha:
# Z covCN q C6AA α(0)
1 8 O 1.613 -0.568 24.435 6.672
2 1 H 0.806 0.284 0.771 1.379
3 1 H 0.806 0.284 0.771 1.379
The C6, C8 and alpha coefficients are denoted explicitly in a.u.:
Mol. C6AA /au·bohr⁶ : 44.553640
Mol. C8AA /au·bohr⁸ : 796.459844
Mol. α(0) /au : 9.429351
Wiberg bond orders:
Wiberg/Mayer (AO) data.
largest (>0.10) Wiberg bond orders for each atom
total WBO WBO to atom ...
1 O 1.839 H 3 0.919 H 2 0.919
2 H 0.919 O 1 0.919
3 H 0.919 O 1 0.919
Molecular dipole and quadropole moments. The contributions are seperated into their respective cartesian dimensions. ‘Full’ represents the corresponding contributions of the molecular dipole or quadropole moments.
molecular dipole:
x y z tot (Debye)
q only: 0.481 0.000 0.340
full: 0.696 0.000 0.492 2.167
molecular quadrupole (traceless):
xx xy yy xz yz zz
q only: 0.305 0.000 -0.916 -0.432 0.000 0.610
q+dip: 0.390 0.000 -1.177 -0.563 0.000 0.787
full: 0.495 -0.000 -1.436 -0.632 -0.000 0.942
All is summed up in the end in both GFN-xTB versions:
-------------------------------------------------
| TOTAL ENERGY -5.070322476938 Eh |
| GRADIENT NORM 0.019484395925 Eh/α |
| HOMO-LUMO GAP 14.652302902752 eV |
-------------------------------------------------
Density Properties¶
Cube Files¶
The xtb program is able to calculate the density, spin-density and the fractional occupation number weighted density (FOD).
For these caclualtions, the program first creates a proper cube grid. The corresponding file is created in your working directory and marked as .cub file.
It provides density and step size informations. An overview is already given in the printout:
cube file module (SG, 7/16)
cube_pthr : 0.050
cube_step : 0.400
non-zero P (%): 76.190 nmat: 16
Grid Boundaries (x y z) :
4.69257109135830 3.00000000000000 4.79524030780751
-3.00000000000000 -3.00000000000000 -3.59840693802375
Total # of points 6720
writing density.cub
cpu time for cube 0.01 s
wall time for cube 0.01 s
Here, various information are provided, like the density matrix neglect threshold cube_pthr and the grid step size cube_step (in Bohr). These values can be changed in the input (xcontrol) file (Detailed Input).
For visualization, programs like chimera can be used, for which the .cub file can be loaded as volume data.
Density and Spin-Density¶
To calculate the density or the spin denisty, the input (xcontrol) file has to be manipulated. Here, the bools density='bool'
or respectively spin density='bool' have to be set to 'true'. This will create a .cub cube file, where the corresponding information is gathered.
For visualization, programs like chimera can be used, for which the .cub file can be loaded as volume data.
Fractional Occupation Density (FOD) calculation¶
The fractional occupation density analysis (FOD) is a diagnostic scheme that displays the static electron correlation localized on a molecule. The density is hereby obtained by performing a computationally cheap Finite-Temperature DFT computation. The electrons are therefore self-consistenly smeared over the molecular orbitals according to a Fermi-Dirac distribution. For a more detailed insight and the theory behind the FOD analytics, please see the original publication. To use FOD for selecting active spaces in CASSCF calculations, refer to our later work on this topic.
To access the FOD analysis, simply use the flag --fod or set fod='true' in the input (xcontrol) file. This will create a fod.cub file and calculate the FOD on the cube grid.
Be sure to set the electronic temperature to a higher value, e.g. 5000 K (--etemp 5000). The FOD population will be displayed in the printout section as:
NFOD : 0.6698
Loewdin FODpop n(s) n(p) n(d)
1 C 0.1924 0.018 0.175 0.000
2 C 0.0673 0.003 0.064 0.000
3 C 0.0673 0.003 0.064 0.000
4 C 0.1924 0.018 0.175 0.000
5 C 0.0673 0.003 0.064 0.000
6 C 0.0673 0.003 0.064 0.000
7 H 0.0039 0.004 0.000 0.000
8 H 0.0039 0.004 0.000 0.000
9 H 0.0039 0.004 0.000 0.000
10 H 0.0039 0.004 0.000 0.000
The NFOD number indicates the static electon correlation
If you do not want to write a full fod.cub file, but still want to analyse the FOD population at least qualitatively, change the fod population ='bool' in the input (xcontrol) file to true. This will display the fractional loewdin
population of the system (see above) and only writes the fod file, where this information is stored.
Redirecting Property Printout¶
For large systems the property printout can become quite lenghty and will
clutter maybe thousands of lines in the standard output.
One possibility is to rigourously deactivate all printouts using the
$write instruction in the input file,
but if one might need this information later it is hard to recover,
as an alternative the property printout can be redirected.
Simply add
$write
output file=properties.out
to your input and specify the name for the redirection. The calculations of the properties are performed as usual but the standard output will show something like
Property printout bound to 'properties.out'
instead of the header, the usual printout can be found in properties.out.
In the file the command line call and current time is saved additionally to
ensure that the printout is reproducable.
Machine Readable Data Dump¶
xtb is able to dump parts of the calculated data in a machine-readable way
using the json-format. To activate the dump into a json file use the input
$write
json=true
which will write a xtbout.json file containing partial charges,
cumulative atomic multipole moments, occupation number and orbtial energies
for single point calculations or frequencies, reduced masses and IR intensities
from hessian calculations.
Geometry Optimization¶
The basics of calculating geometry optimizations with xtb are presented in this chapter.
Please check out the chapter Singlepoint Calculations for options that are not optimization-specific, as the charge or the number of SCF iterations, for example. Solvation can be included easily by using ALPB. For this approach, please read the chapter Implicit Solvation.
Contents
Optimization levels¶
xtb has a build-in geometry optimizer called approximate normal coordinate rational function optimizer (ANCopt) which uses a Lindh-type model Hessian to generate an approximate normal coordinate system. It is activated by the flag --opt [level]. The following levels are available:
level |
Econv/Eh |
Gconv/Eh·α⁻¹ |
Accuracy |
|---|---|---|---|
crude |
5 × 10⁻⁴ |
1 × 10⁻² |
3.00 |
sloppy |
1 × 10⁻⁴ |
6 × 10⁻³ |
3.00 |
loose |
5 × 10⁻⁵ |
4 × 10⁻³ |
2.00 |
lax |
2 × 10⁻⁵ |
2 × 10⁻³ |
2.00 |
normal |
5 × 10⁻⁶ |
1 × 10⁻³ |
1.00 |
tight |
1 × 10⁻⁶ |
8 × 10⁻⁴ |
0.20 |
vtight |
1 × 10⁻⁷ |
2 × 10⁻⁴ |
0.05 |
extreme |
5 × 10⁻⁸ |
5 × 10⁻⁵ |
0.01 |
Here, energy convergence (Econv) is the allowed change in the total energy at convergence and the gradient convergence (Gconv) the allowed change in the gradient norm at convergence. The accuracy
is handed to the singlepoint calculations for integral cutoffs and self consistent field convergence criteria. It is adjusted to fit the geometry convergence thresholds automatically.
The maximal number of optimization cycles can be defined by using the flag --cycles integer. By default, the optimization level ‘normal’ is used.
The maximum number of optimization cycles is usually automatically determined at runtime from the total degrees of freedoms and is at least 200 and at most 10000.
Running a geometry optimization¶
Example 1: ethyne¶
Input structures in TURBOMOLE (coord) or Xmol coordinates can be optimized. An example xyz input for ethyne is (e.g. inp.xyz):
4
H 0.00 0.00 0.00
C 0.00 0.00 1.00
C 0.00 0.00 2.00
H 0.00 0.00 3.00
For running the geometry optimization using the defaults, call
> xtb inp.xyz --opt
A singlepoint calculation is performed. Then, the optimization setup is printed:
-----------------------------------------------------------
| ===================== |
| A N C O P T |
| ===================== |
| Approximate Normal Coordinate |
| Rational Function Optimizer |
-----------------------------------------------------------
...................................................
: SETUP :
:.................................................:
: optimization level normal :
: max. optcycles 200 :
: ANC micro-cycles 20 :
: degrees of freedom 7 :
:.................................................:
: RF solver spevx :
: input Hessian false :
: write xtbopt.log true :
: linear (good luck) true :
: energy convergence 0.5000000E-05 Eh :
: grad. convergence 0.1000000E-02 Eh/α :
: maximium RF displ. 1.0000000 :
: Hlow (freq-cutoff) 0.2000000E-01 :
: Hmax (freq-cutoff) 5.0000000 :
: S6 in model hess. 20.0000000 :
...................................................
This is followed by the printout of the optimization cycles. Here every 20 cycles the ANC coordinate system will be reset and an additional short summary block regarding the progress in the last few cycles will be shown.
........................................................................
.............................. CYCLE 1 ..............................
........................................................................
1 -5.5172337 -0.551723E+01 0.160E-07 11.16 0.0 T
2 -5.5172337 -0.266454E-14 0.611E-08 11.16 100000.0 T
3 -5.5172337 0.177636E-14 0.173E-08 11.16 100000.0 T
SCC iter. ... 0 min, 0.000 sec
gradient ... 0 min, 0.000 sec
* total energy : -5.0806015 Eh change 0.8185541E-10 Eh
gradient norm : 1.0710691 Eh/α predicted 0.0000000E+00 (-100.00%)
displ. norm : 0.4065773 α lambda -0.3521146E+00
maximum displ.: 0.3123635 α in ANC's #3, #7, #4, ...
........................................................................
.............................. CYCLE 2 ..............................
........................................................................
Tip
you can find information about the accuracy of the BFGS model of the PES at each optimization step and the error between predicted and actual change in energy.
Note
the displacement summary at each step refers always to the next optimization cycle.
The convergence of the geometry optimization is confirmed by the printout
*** GEOMETRY OPTIMIZATION CONVERGED AFTER 6 ITERATIONS ***
Afterwards, a final singlepoint calculation is performed (including a property printout). The total energy and the name of the file containing the optimized coordinates are printed at the end of the output:
optimized geometry written to: xtbopt.xyz
-------------------------------------------------
| TOTAL ENERGY -5.206771946579 Eh |
| GRADIENT NORM 0.000476954973 Eh/α |
| HOMO-LUMO GAP 7.289739001449 eV |
-------------------------------------------------
Note
The input coordinates are not overwritten by xtb. The optimized geometry can be found either in the file xtbopt.xyz or xtbopt.coord depending on the format of the input.
The file xtbopt.xyz for this example looks like:
4
SCF done -5.206771946579 0.000476954973
H 0.00000000000000 -0.00000000000000 -0.14662251809779
C -0.00000000000000 0.00000000000000 0.90317992211836
C -0.00000000000000 0.00000000000000 2.09682010367354
H -0.00000000000000 0.00000000000000 3.14662249230588
Further, a trajectory of the geometry optimization written in Xmol format (even if the input was a coord file) is written to the file xtbopt.log.
Example 2: cyclopentadienyl anion¶
The second example is a geometry optimization of Cp⁻. The input coordinates are far from a planar structure and are given in TURBOMOLE format as coord file.
$coord
0.00000000000000 0.00000000000000 0.00000000000000 c
0.00000000000000 0.00000000000000 2.92151660144120 c
2.85226569757548 0.00000000000000 3.55384920112287 c
3.90292319184177 2.03158598395524 1.73614809006603 c
2.27186844120391 1.64373103353725 -0.65644172568502 c
-0.86886206083043 1.75686326793472 3.63081207733690 h
3.11610359107057 0.44206741371820 5.57363951455663 h
5.95582339684982 1.75824654746399 1.50061262486316 h
3.42008871625882 0.73590659929899 -2.14036617906866 h
0.31080892625410 -1.94044071311390 -0.69474836412474 h
$end
Now, the optimization level tight and a maximal number of 50 optimization cycles is chosen. This is done for teaching purposes only.
> xtb coord --opt tight --cycles 50 --charge -1
The ANCopt setup is adjusted as follows:
...................................................
: SETUP :
:.................................................:
: optimization level tight :
: max. optcycles 50 :
: ANC micro-cycles 20 :
: degrees of freedom 24 :
:.................................................:
: RF solver spevx :
: input Hessian false :
: write xtbopt.log true :
: linear? false :
: energy convergence 0.1000000E-05 Eh :
: grad. convergence 0.8000000E-03 Eh/α :
: maximium RF displ. 1.0000000 :
: Hlow (freq-cutoff) 0.2000000E-01 :
: Hmax (freq-cutoff) 5.0000000 :
: S6 in model hess. 20.0000000 :
...................................................
The geometry optimization is converged after 22 iterations. The optimized coordinates are written to the file xtbopt.coord.
$coord
0.44060377782450 -0.01412168126920 0.18353526062450 C
0.29759594746033 0.20416120151187 2.80401943168676 C
2.63965610517835 1.02998458234760 3.68100113536889 C
4.22999047646770 1.32233523397087 1.60243655937779 C
2.87122906158385 0.67587612191465 -0.55901104575941 C
-1.35063621036312 -0.20020256016136 3.96194626998985 H
3.13809669169362 1.38388424380555 5.64254720998168 H
6.18714478782806 1.94516496134903 1.65710127132652 H
3.58252077369211 0.70464340056577 -2.48621742790732 H
-1.07518151114132 -0.62376537124033 -1.06233682418088 H
$end
Example 3: p-benzyne in toluene¶
As third example, the geometry optimization of p-benzyne in the triplet state solved in toluene is presented. The following input structure saved as inp.xyz is utilized:
10
C 0.000000 0.000000 0.000000
C 0.000000 0.000000 1.400000
C 1.212436 0.000000 2.100000
C 2.424871 0.000000 1.400000
C 2.424871 0.000000 0.000000
C 1.207822 -0.105671 -0.700000
H -0.910967 0.244093 1.944500
H 1.219600 0.163768 3.176592
H 3.367973 0.000000 -0.544500
H 1.207822 -0.105671 -1.789000
The number of unpaired electrons (uhf) and the solvent have to be specified. Further, the optimization level ‘loose’ is chosen here for teaching purposes.
> xtb inp.xyz --opt loose --alpb toluene --uhf 2
The thresholds corresponding to the optimization level ‘loose’ can be found in the ANCopt setup.
...................................................
: SETUP :
:.................................................:
: optimization level loose :
: max. optcycles 200 :
: ANC micro-cycles 20 :
: degrees of freedom 24 :
:.................................................:
: RF solver spevx :
: input Hessian false :
: write xtbopt.log true :
: linear? false :
: energy convergence 0.5000000E-04 Eh :
: grad. convergence 0.4000000E-02 Eh/α :
: maximium RF displ. 1.0000000 :
: Hlow (freq-cutoff) 0.2000000E-01 :
: Hmax (freq-cutoff) 5.0000000 :
: S6 in model hess. 20.0000000 :
...................................................
The geometry optimization converges after five iterations, resulting in the following coordinates (written to the file xtbopt.xyz):
10
SCF done -14.662320537665 0.001879475862 ! total energy in Eh and gradient norm in Eh/α
C 0.07867071152305 0.00730041248664 0.04608303752229
C 0.00150775744363 0.08123575674794 1.41160138347040
C 1.21188251791186 0.08194614686924 2.10875452439614
C 2.35260556407908 0.02986595253321 1.35144422933203
C 2.43040668441166 -0.03018610417618 -0.01499810496837
C 1.21898702608881 -0.05479836016580 -0.71052501252580
H -0.94612623103426 0.13538712165891 1.93110285483949
H 1.23696707333528 0.12186857053414 3.18813400290200
H 3.37737604916301 -0.05932253738648 -0.53517807393770
H 1.19215084707789 -0.11677795910162 -1.78882684103049
Convergence problems¶
The failure of the geometry convergence is indicated by the printout
*** FAILED TO CONVERGE GEOMETRY OPTIMIZATION IN 500 ITERATIONS ***
Additionally, the empty file NOT_CONVERGED is written. If convergence problems in the SCC occur, it is recommended to start with GFN0-xTB which does not have to perform SCC iterations. Then the geometry optimization can be improved using GFN2-xTB.
It can occur sometimes that a geometry does not converge correctly or at all if the calculation is carried out in the gas phase. It is recommended to use ALPB in this cases. An example for the difference made by using ALPB during the geometry optimization can be seen below. If the system is optimized in chloroform, the chloride anion coordinates the cation while the neutral compounds are formed in the gas phase.
optimized in the gasphase¶
optimized in chloroform¶
Optimization Engines¶
Note
feature implemented in version 6.1.4
xtb offers different optimizers which can be switched using the detailed
input with
$opt
engine=<name>
possible optimizers are
- Approximate Normal Coordinate Rational Function optimizer (ANCopt)
engine=rf(default)rational function for optimal step
BFGS update of Hessian
approximate normal coordinate system
- L-BFGS Approximate Normal Coordinate optimizer (L-ANCopt)
engine=lbfgsL-BFGS step and update of Hessian
approximate normal coordinate system
- Fast Inertial Relaxation Engine (FIRE)
engine=inertialMD propagation with preconditioning
BFGS update of Hessian
cartesian coordinate system
Exploration of the potential energy surface (PES)¶
Contents
Input¶
xtb can be used to scan the potential energy surface. It is possible to adjust distances as well as angles and the dihedral angles via the xcontrol file. To scan the potential energy surface, you first have to optimize your molecule. Then you have to find out the atom numbers you wish to constrain and write them to your xcontrol file (see examples later). There are two different ways to modify your xcontrol.
First constrain your geometry, using the $constrain block, then scanning using the $scan block.
Constrain and scan in one step, only using the $scan block.
Both will do exactly the same within your calculation. Lastly you have to run an optimization.
Note
xtb uses force constants to constrain the geometry. Therefore the geometry data you use for the scan can deviate from your given input during the optimization. It is not possible to scan the potential energy surface without doing an optimization. In consequence, it is always a relaxed surface scan.
Dihedral angle scan¶
Ethane¶
Let’s start with an easy example. You all know the potential energy surface of a dihedral angle scan of ethane, so this is a good start to check, if you are doing everything right. The following is a converged ethane structure given as xyz file.
> cat ethane.xyz
8
-7.46994680
C -0.01503441120750 0.04820403778911 -0.01075686629161
H -0.02618280545732 0.12324247717853 1.07751478989514
H 1.02025706611374 0.10521724412205 -0.34995019287160
H -0.56108089374185 0.89840506905011 -0.42160774836772
C -0.65104926960692 -1.26213120711759 -0.46045958867132
H -1.67328207424848 -1.33815676349645 -0.08720971228148
H -0.67543548798470 -1.32088660386766 -1.54947400918083
H -0.08161812386697 -2.11204925365809 -0.08140067223057
To scan the dihedral angle I choose the atoms 1 (first carbon), 5 (second carbon), 4 (hydrogen at first carbon) and 8 (hydrogen at second carbon). The dihedral angle is therefore between 8, 5, 1, 4 or vice versa. Now you have to modify your input. As I already said, there are two different ways to scan the PES.
Constrain and scan in two steps
> cat scan.inp
$constrain
force constant=0.05
dihedral: 8,5,1,4,60.0
$scan
1: 60.0,420.0,72
$end
The $constrain will fix the dihedral between atom 8, 5, 1 and 4 to 60.0 degrees. It is also possible to change the force constant used to constrain the geometry. For further hints see chapter Detailed Input: Fixing, Constraining and Confining - Constraining Potentials. Afterwards a scan is conducted with the 1. constraint (in this case the dihedral) from 60.0 to 420.0 degrees in 72 steps.
The constraint can also be done on-the-fly
$constrain
force constant=0.05
$scan
dihedral: 8,5,1,4,60.0; 60.0,420.0,72
$end
The part up to the semicolon (dihedral: 8,5,1,4,60.0) is passed to the $constrain instruction and evaluated there, and afterwards a scan with this constraint is conducted from 60.0 to 420.0 degrees in 72 steps.
Which methods you want to use is up to you, as they are doing exactly the same.
Now you are ready to start the calculation.
> xtb ethane.xyz --opt --input scan.inp
The calculation gives the usual files described in the other chapters, and an extra file called xtbscan.log. This is a file in XMol format, which can be read by e.g. molden. All optimized structures of the scan and their energy are written to that file, so it contains in our case 72 structures, starting and ending like this:
> cat xtbscan.log
8
SCF done -7.33636977
C -0.016167577954 0.046756019273 -0.010925351519
H -0.722837769279 0.635952345713 0.569507202626
H 0.858799528033 -0.144587130449 0.606495402607
H 0.295104980741 0.636307029349 -0.871373313682
C -0.649893664036 -1.261548762672 -0.459251334661
H -0.962364182156 -1.850869022139 0.400300369375
H -1.523304826531 -1.069936539515 -1.078572301721
H 0.057237511182 -1.850228939559 -1.039524673024
8
SCF done -7.33633301
C -0.014508419361 0.046085202187 -0.010980431860
H -0.712592003942 0.622234788963 0.592857532524
H 0.875734542981 -0.143892036194 0.583801797058
H 0.267743868859 0.650856540715 -0.870728921217
C -0.650432967813 -1.260775477944 -0.461051561431
H -0.987374035660 -1.836977921850 0.398253949047
H -1.507838805925 -1.070682914383 -1.102253264664
H 0.065841820861 -1.865003181495 -1.013243099455
8
SCF done -7.33622104
C -0.013197790454 0.045694504417 -0.011256531141
H -0.701582052023 0.608208846300 0.616415577820
H 0.892470173219 -0.143385451024 0.559597860026
H 0.239350600054 0.665739016442 -0.869355008077
C -0.650618419000 -1.260384104771 -0.462367255784
H -1.013262191587 -1.822961711987 0.395720305781
H -1.490594450886 -1.071189460974 -1.126101769970
H 0.074008130676 -1.879876638403 -0.985997178655
...
...
...
8
SCF done -7.33622017
C -0.013004744475 0.045540690542 -0.011114232961
H 1.030144565230 0.090508635597 -0.314432978298
H -0.533071797992 0.894833527576 -0.449705894194
H -0.065637709250 0.143792574844 1.071609413617
C -0.651185106898 -1.260114193001 -0.462340695966
H -0.711362672977 -1.305688812601 -1.547024982931
H -0.064980472761 -2.109392137114 -0.117000615435
H -1.654328060878 -1.357635285842 -0.053334013833
8
SCF done -7.33633308
C -0.014346704593 0.046121859404 -0.011308096497
H 1.020906551190 0.102932886427 -0.339872745036
H -0.551739904813 0.895891227197 -0.426589805208
H -0.037115500933 0.129430347168 1.073605709020
C -0.650547319963 -1.260694835302 -0.461135641012
H -0.684295266226 -1.318119390348 -1.546743615925
H -0.080580374590 -2.110437772732 -0.091714398274
H -1.665707480072 -1.343279321813 -0.079585407068
8
SCF done -7.33637035
C -0.015578067243 0.046627972173 -0.011197389104
H 1.010992111828 0.115268321609 -0.364499843825
H -0.569593214036 0.896318028100 -0.403610362573
H -0.008392561436 0.115840454214 1.074947192037
C -0.650244617685 -1.261196821401 -0.459943193673
H -0.657767750171 -1.330468135987 -1.545565118941
H -0.096332291574 -2.110841034948 -0.067236403729
H -1.676509609683 -1.329703783762 -0.106238880192
The resulting scan as well as the resulting energy curve are shown.
Dihedral scan of ethane.¶
Energy diagram of the dihedral scan of ethane.¶
1-Bromo-2-chloroethane¶
xtb is also able to constrain and scan at the same time. The optimized input structure in this case (the above named disubstituted ethane) is shown below.
> cat start.xyz
8
C 0.01774700194036 0.02394056724825 0.01171709768115
H 0.02320553063247 0.04452098239361 1.10173147789467
H 1.04534455713418 0.04827808072517 -0.35142167075981
CL -0.81853417509556 1.48223297221309 -0.57258786378603
C -0.70382290601220 -1.19970227294247 -0.49854993198382
H -1.73033497415121 -1.22321931753990 -0.13963544593745
H -0.70258146165504 -1.22676776606289 -1.58588899303155
BR 0.20555042720700 -2.80743824603485 0.15129132992284
Now, the input can be modified. The modification shown below are only for training purposes, so they don’t have to make any sense.
$constrain
distance: 1,5,auto
dihedral: 8,5,1,4,60.0
$scan
2: 60.0,780.0,100
$opt
maxcycle=5
$end
I chose to firstly set the constraints and then the scanning part. The constraints are written one after another. The first constraint keeps the distance of atom 1 and atom 5 (both carbons) to their actual value, whereas the second one constrains the dihedral angle of atoms 8, 5, 1 and 4 to 60.0°. In the scan block, the second constraint is changed from 60.0° to 780.0° in 100 steps. The maximum cycle of the optimization is set in the $opt part to 5. Consequently the optimization has not much steps to shift the constrained atoms. All in all, the chosen settings results in the following.
Scan of the dihedral angle between chloride and bromide of the disubstituted ethane.¶
Energy diagram of the dihedral scan.¶
Angle and Distance scan¶
Ammonia¶
Concerted Scan¶
It is of course also possible to scan along angle and distance. Therefore in the next example, the angle and the distance is scanned in one scan. If you want to scan all options simultaneously, you have to use the mode=concerted option in the $scan block. It requires, that the number of steps in the scan is always the same, otherwise xtb will exit in error.
The optimized input geometry is written below.
> cat ammonia.xyz
4
N -0.00990404770994 -0.01698500657667 -0.00712107610609
H 0.00434306677482 0.00733732515324 1.00490910707310
H 0.94901246801925 0.00720047578638 -0.33083175918033
H -0.46827248708413 0.82547620563705 -0.33095427178668
Now, the constraining and the scanning options are set in the input file.
$constrain
force constant=0.5
distance: 1, 4, 0.5
angle: 2, 1, 3, 150.0
dihedral: 2, 1, 3, 4, auto
$scan
mode=concerted
# different steps for each constraint!
1: 0.5, 1.4, 50
2: 150.0, 90.0, 60
$opt
maxcycle=5
$end
The constraint of the dihedral angle between all given atoms to their actual value was set, since otherwise the first optimization would lead to a planar molecule. As you can see, I chose mode=concerted, but different number of steps for the scan. Since a concerted scan can only performed if all scans are performed with the same number of steps, xtb should exits in error, of course it does printing the message:
#ERROR! Wrong setup for concerted scan, aborting...
Note
A concerted scan can only carried out if all constraints are scanned with the same number of steps.
The correct input is given below.
$constrain
force constant=0.5
distance: 1, 4, 0.5
angle: 2, 1, 3, 150.0
dihedral: 2, 1, 3, 4, auto
$scan
mode=concerted
1: 0.5, 1.4, 60
2: 150.0, 90.0, 60
$opt
maxcycle=5
$end
The resulting path can be seen in the following movie.
Note
Nobody stops you from scanning the same constraint twice, this usually does not make much sense for concerted scans, but is not catched by the parser.
Sequential Scan¶
Another way to scan would be in sequential mode. xtb will then scan along all constraints one after the other, always leaving the last scanned constraint at it last value. An example input can look like this, using the ammonia example from above.
$constrain
force constant=0.5
distance: 1, 2, 0.5
angle: 4, 1, 3, 140.0
dihedral: 2, 1, 3, 4, auto
$scan
mode=sequential
2: 140.0, 90.0, 40
1: 0.5, 2.0, 60
$opt
maxcycle=5
The mode=sequential flag is the default value for scans, due to the nature of the scan different step sizes are possible here.
Note
There is no multidimensional scan supported on purpose since they tend to be expensive on high-dimensional potential energy surfaces and are difficult to visualize. But they can be easily constructed, by repeatly scanning the same constraint.
I chose to firstly scan along the angle and then along the distance. The resulting path can be seen below.
Tip
If your resulting path oscillates at some point, try to increase the number of maximum cycles maxcycle in your $opt block. Sometimes xtb just needs more steps to properly converge your structure.
Implicit Solvation¶
In this chapter, all neccessary information will be given in order to use the implicit solvent model ALPB in xTB calculations. Parameterized solvents and available grids are given as well.
Contents
General command-line control¶
Note
The ALPB solvation model is implemented in version 6.3.3 or newer, use --gbsa in older versions instead.
The analytical linearized Poisson-Boltzmann (ALPB) model is envoked with the flag --alpb [Solvent].
As an example the single point calculation employing the ALPB model for solvation in water would be started by
> xtb coord --alpb water
As an example the energy printout of a singlepoint calculation of a H₂O molecule in implicit water is given.
:::::::::::::::::::::::::::::::::::::::::::::::::::::
:: SUMMARY ::
:::::::::::::::::::::::::::::::::::::::::::::::::::::
:: total energy -5.080052453799 Eh ::
:: total w/o Gsasa/hb -5.072629830168 Eh ::
:: gradient norm 0.004391355361 Eh/α ::
:: HOMO-LUMO gap 14.784541887474 eV ::
::.................................................::
:: SCC energy -5.113963912352 Eh ::
:: -> isotropic ES 0.042951967946 Eh ::
:: -> anisotropic ES -0.000414697277 Eh ::
:: -> anisotropic XC -0.000390138125 Eh ::
:: -> dispersion -0.000131341861 Eh ::
:: -> Gsolv -0.011759733450 Eh ::
:: -> Gborn -0.004337109820 Eh ::
:: -> Gsasa 0.000220003644 Eh ::
:: -> Ghb -0.009500070401 Eh ::
:: -> Gshift 0.001857443127 Eh ::
:: repulsion energy 0.033911458523 Eh ::
:: add. restraining 0.000000000000 Eh ::
:::::::::::::::::::::::::::::::::::::::::::::::::::::
The solvation free energy is printed as Gsolv and is also added
to all total energy printouts.
Optimizing a geometry with the ALPB model can be done with the following input
> xtb coord --opt --alpb water
The order of the flags can be altered and the input
is not case sensitive.
Like in a optimization without ALPB the optimized coordinates are
written to a new file (xtbopt.coord).
In General the ALPB can be used in combination with all available run types
implemented in the xtb.
Parameterized Solvents¶
The ALPB model is parameterized for the Hamiltonian of GFN1-xTB, GFN2-xTB, and the GFN-FF, but not for GFN0-xTB. For the GFN1-xTB and GFN2-xTB Hamltonians also a generalized Born (GB) model with surface area (SA) contributions, dubbed GBSA is available. Here is a list of the available solvents.
solvents |
GFN1(ALPB) |
GFN1(GBSA) |
GFN2(ALPB) |
GFN2(GBSA) |
GFN-FF |
|---|---|---|---|---|---|
Acetone |
x |
x |
x |
x |
x |
Acetonitrile |
x |
x |
x |
x |
x |
Aniline |
x |
x |
x |
||
Benzaldehyde |
x |
x |
x |
||
Benzene |
x |
x |
x |
x |
x |
CH₂Cl₂ |
x |
x |
x |
x |
x |
CHCl₃ |
x |
x |
x |
x |
x |
CS₂ |
x |
x |
x |
x |
x |
Dioxane |
x |
x |
x |
||
DMF |
x |
x |
x |
||
DMSO |
x |
x |
x |
x |
x |
Ether |
x |
x |
x |
x |
x |
Ethylacetate |
x |
x |
x |
||
Furane |
x |
x |
x |
||
Hexandecane |
x |
x |
x |
||
Hexane |
x |
x |
x |
x |
|
Methanol |
x |
x |
|||
Nitromethane |
x |
x |
x |
||
Octanol |
x |
x |
x |
||
Octanol (wet) |
x |
x |
x |
||
Phenol |
x |
x |
x |
||
Toluene |
x |
x |
x |
x |
x |
THF |
x |
x |
x |
x |
x |
Water (H₂O) |
x |
x |
x |
x |
x |
To get the legacy GBSA model setup a detailed input with
$gbsa
kernel=still
and invoke the program with the --gbsa flag instead of the --alpb flag.
Available Grids¶
Different Lebedev grids for the calculation of the SASA term are
implemented in xtb. The grids are independent of the used GFNn method
and are set in the detailed input as
$gbsa
gbsagrid=tight
The default grid level is normal.
The available grid levels are given in the table below
with the corresponding number of gridpoints.
Gridlevel |
Gridpoints |
|---|---|
normal |
230 |
tight |
974 |
verytight |
2030 |
extreme |
5810 |
Larger grids increase the computation time and reduce numerical noise in the energy. They may help to converge geometry optimizations with ALPB for large molecules which would otherwise not converge due to numerical noise.
Reference States¶
The default reference state option is bar1M which should not
be changed for normal production runs.
In order to compare the solvation free energy with
solvation free energies from COSMO-RS the reference state can be set to reference which corresponds
to the same reference option as in COSMO-RS. This could be done with
> xtb coord --opt --alpb water reference
Extended Functionality¶
Solvent Accessable Surface Area¶
Note
feature implemented in version 6.2
To get more insights and diagnostics for a ALPB calculation the Born radii and the solvent accessable surface area can be printed by toggling the property-printout with
$write
gbsa=true
The printout for a branched octane isomer using ALPB(Water) looks like
* generalized Born model for continuum solvation
# Z Born rad/ŠSASA/Ų H-bond
1 6 C 3.761 0.000 0.000
2 6 C 3.761 0.000 0.000
3 6 C 2.741 1.820 -0.000
4 6 C 2.741 1.839 -0.000
5 6 C 2.741 1.817 -0.000
6 6 C 2.741 1.820 -0.000
7 6 C 2.741 1.839 -0.000
8 6 C 2.741 1.817 -0.000
9 1 H 2.136 11.404 -0.015
10 1 H 2.130 12.571 -0.017
11 1 H 2.098 14.966 -0.020
12 1 H 2.130 12.563 -0.017
13 1 H 2.098 14.979 -0.020
14 1 H 2.136 11.403 -0.015
15 1 H 2.136 11.412 -0.015
16 1 H 2.130 12.524 -0.017
17 1 H 2.098 14.948 -0.020
18 1 H 2.136 11.404 -0.015
19 1 H 2.130 12.571 -0.017
20 1 H 2.098 14.966 -0.020
21 1 H 2.130 12.563 -0.017
22 1 H 2.098 14.979 -0.020
23 1 H 2.136 11.403 -0.015
24 1 H 2.136 11.412 -0.015
25 1 H 2.130 12.524 -0.017
26 1 H 2.098 14.948 -0.020
total SASA / Ų : 244.491
The quartary carbon atoms are shown with no solvent accessable surface area, which means they are completely buried in the molecule leading to large Born radii.
Calculation of Vibrational Frequencies¶
In this chapter, all necessary information about the calculation of vibrational spectra and thermostatistical contributions are given.
Contents
Performing simple Vibrational Frequency calculations¶
Vibrational frequency calculations are available only through two-sided numerical differentiation of analytical gradients.
Consider a simple example like the following hydrogen abstraction reaction:
7
C -0.12888312425142 -0.00640246259879 -0.00997057133406
H 1.44011699709596 0.12229812355524 -0.02854203428735
H -0.41612454870604 1.02694842152161 -0.04938812535015
H -0.26306601703832 -0.58286887757121 -0.90445094952445
H -0.26440375738028 -0.51708010658031 0.92386857306799
O 2.45008586500521 0.26032015001761 0.01133571198248
H 2.61210033905108 0.98358191645276 0.62026402303033
By invoking the --hess command line argument, xtb executes a calculation of the Hessian matrix. The --ohess keyword may be used instead if a prior optimization of the structure is desired.
xtb min.xyz --hess --uhf 1
At the end of the frequency job you get an output like this:
-------------------------------------------------
| Frequency Printout |
-------------------------------------------------
projected vibrational frequencies (cm-1)
eigval : -0.00 -0.00 -0.00 0.00 0.00 0.00
eigval : 40.69 211.99 360.40 405.89 601.08 759.17
eigval : 829.07 1371.91 1375.70 1477.42 2297.37 3115.69
eigval : 3190.88 3197.05 3648.64
reduced masses (amu)
1: 4.63 2: 12.19 3: 12.31 4: 9.70 5: 9.30 6: 12.74 7: 1.74 8: 12.17
9: 1.45 10: 1.77 11: 1.92 12: 1.45 13: 2.39 14: 2.02 15: 2.03 16: 2.07
17: 2.17 18: 1.07 19: 2.09 20: 2.09 21: 1.86
IR intensities (amu)
1: 0.17 2: 0.46 3: 0.44 4: 0.41 5: 0.08 6: 0.35 7: 0.48 8: 0.26
9: 0.26 10: 0.27 11: 0.25 12: 0.41 13: 0.30 14: 0.04 15: 0.07 16: 0.52
17: 0.51 18: 0.06 19: 0.14 20: 0.12 21: 0.18
Raman intensities (amu)
1: 0.00 2: 0.00 3: 0.00 4: 0.00 5: 0.00 6: 0.00 7: 0.00 8: 0.00
9: 0.00 10: 0.00 11: 0.00 12: 0.00 13: 0.00 14: 0.00 15: 0.00 16: 0.00
17: 0.00 18: 0.00 19: 0.00 20: 0.00 21: 0.00
output can be read by thermo (or use thermo option).
writing <g98.out> molden fake output.
recommended (thermochemical) frequency scaling factor: 1.0
This output consists of the calculated vibrational frequencies and the vibrational modes. In the example above there are six frequencies which are identically zero. These frequencies correspond to the rotations and translations of the molecule. They have been projected out of the Hessian before the calculation of the frequencies and thus, the zero values do not tell you anything about the quality of the Hessian that has been diagonalized.
xtb writes an g98.out file in GAUSSIAN-format, which can be opened with the popular MOLDEN program to visualize the vibrational modes.
Further, a hessian file is written, containing the projected Hessian matrix in turbomole format.
Calculation of thermochemical properties¶
Each frequency job provides the thermochemical properties at 298.15 K. (for other temperatures, see below). No further user-input is required to obtain all important thermostatistical contributions. The contributions are calculated following a coupled rigid-rotor-harmonic-oscillator approach. If a molecular symmetry is detected, the resulting rotational number is automatically accounted for. The symmetry detection can be adjusted in the $symmetry block of the xcontrol file if necessary.
-------------------------------------------------
| Thermodynamic Functions |
-------------------------------------------------
...................................................
: SETUP :
:.................................................:
: # frequencies 15 :
: # imaginary freq. 0 :
: linear? false :
: only rotor calc. false :
: symmetry C1 :
: rotational number 1 :
: scaling factor 1.0000000 :
: rotor cutoff 50.0000000 cm⁻¹ :
: imag. cutoff -20.0000000 cm⁻¹ :
:.................................................:
mode ω/cm⁻¹ T·S(HO)/kcal·mol⁻¹ T·S(FR)/kcal·mol⁻¹ T·S(vib)
------------------------------------------------------------------------
1 40.69 -1.55795 ( 30.48%) -1.11458 ( 69.52%) -1.24972
2 211.99 -0.60419 ( 99.69%) -0.62804 ( 0.31%) -0.60426
------------------------------------------------------------------------
temp. (K) partition function enthalpy heat capacity entropy
cal/mol cal/K/mol cal/K/mol J/K/mol
298.15 VIB 13.7 1501.827 9.485 9.210
ROT 0.909E+04 888.752 2.981 21.094
INT 0.125E+06 2390.579 12.466 30.304
TR 0.184E+27 1481.254 4.968 36.401
TOT 3871.8331 17.4344 66.7050 279.0936
T/K H(0)-H(T)+PV H(T)/Eh T*S/Eh G(T)/Eh
------------------------------------------------------------------------
298.15 0.617016E-02 0.583013E-01 0.316937E-01 0.266076E-01
------------------------------------------------------------------------
:::::::::::::::::::::::::::::::::::::::::::::::::::::
:: THERMODYNAMIC ::
:::::::::::::::::::::::::::::::::::::::::::::::::::::
:: total free energy -8.613409150740 Eh ::
::.................................................::
:: total energy -8.640016786693 Eh ::
:: zero point energy 0.052131167146 Eh ::
:: G(RRHO) contrib. -0.025523531193 Eh ::
:::::::::::::::::::::::::::::::::::::::::::::::::::::
Multiple temperatures can be calculated using the build in thermodynamic functions calculator by using a input file similar to this
$thermo
temp=150.0,200.0,250.0,273.15,298.15
The final summary looks like
T/K H(0)-H(T)+PV H(T)/Eh T*S/Eh G(T)/Eh
------------------------------------------------------------------------
150.00 0.250495E-02 0.546739E-01 0.135034E-01 0.411705E-01
200.00 0.361203E-02 0.557809E-01 0.192424E-01 0.365386E-01
250.00 0.484240E-02 0.570113E-01 0.253913E-01 0.316200E-01
273.15 0.545010E-02 0.576190E-01 0.283634E-01 0.292557E-01
298.15 0.617016E-02 0.583013E-01 0.316937E-01 0.266076E-01 (used)
------------------------------------------------------------------------
xtb will always use the last entry from the temperature list for all
further calculations and printouts.
Dealing with imaginary modes and non-minimum structures¶
If a frequency calculation is invoked using the --hess command line argument, xTB automatically checks the gradient norm for a non-zero value. For unoptimized structures with significant remaining grad. norm, a warning is printed. If you want xTB to exit with an error code instead of this warning, use the --strict command line argument.
########################################################################
# WARNING! Some non-fatal runtime exceptions were caught, please check:
# - Hessian on incompletely optimized geometry!
########################################################################
A xtbhess.coord file is created in this case, containing the input structure distorted along the imaginary mode. In case of unwanted imaginary modes, this structure can be used as a starting point to perform further optimizations to get rid of the imaginary frequency and locate the true minimum.
Advanced options¶
Of course, the calculated frequencies depend on the masses used for each atom. Several options exist to modify/scale the default atomic masses in the $hess block of the xcontrol file.
$hess
sccacc=real
SCC accuracy level in Hessian runs
step=real
Cartesian displacement increment for numerical Hessian
isotope: int,real
set mass of atom number int to real (synonym to modify mass)
modify mass: int,real
set mass of atom number int to real (synonym to isotope)
scale mass: int,real
scale mass of atom number int by real
element mass: int,real
set mass of elements int to real
Changes regarding sccacc or step should be made with caution, as large displacements or loose SCC accuracy can lead to unreliable frequencies due to excessive numerical noise in the calculations.
The thermostatistical calculations can be influenced by the $thermo block of the xcontrol file.
$thermo
temp=real
temperature for thermostatistical calculation (default: 298.15 K)
sthr=real
rotor cut-off (cm-1) in thermo (default: 50.0)
Single Point Hessian (SPH) calculations¶
A prerequisite for accurate thermostatistics so far was to optimize the molecular input structures in order to avoid imaginary frequencies as discussed above. This inevitably leads to changes in the geometry if different theoretical levels are applied for geometry optimization and frequency calculations. Therefore, we propose a new method termed single-point Hessian (SPH) for the computation of HVF and thermodynamic contributions to the free energy within the modified RRHO approximation for general nonequilibrium molecular geometries. The main publication for SPH can be found at: JCTC.
A SPH calculation is invoked using the --bess command line argument. xTB automatically applies a biasing potential given as Gaussian functions expressed with the RMSD in Cartesian space in order to retain the initial geometry. In the xTB printout this is indicated by e.g.:
metadynamics with 1 initial structures loaded
-------------------------------------------------
| Optimal kpush determination |
-------------------------------------------------
target rmsd / Å 0.100000
unbiased initial rmsd 0.415461
iter. min. max. rmsd kpush
1 0.000000 1.000000 0.023187 -0.500000
2 0.000000 0.500000 0.052359 -0.250000
3 0.000000 0.250000 0.090094 -0.125000
4 0.000000 0.125000 0.135494 -0.062500
5 0.062500 0.125000 0.108071 -0.093750
6 0.093750 0.125000 0.098169 -0.109375
7 0.093750 0.109375 0.102794 -0.101562
8 0.101562 0.109375 0.100426 -0.105469
final kpush: -0.105469
-------------------------------------------------
| Biased Numerical Hessian |
-------------------------------------------------
kpush : -0.10547
alpha : 1.00000
step length : 0.00500
SCC accuracy : 0.30000
Hessian scale factor : 1.00000
frozen atoms in % : 0.00000 0
RMS gradient : 0.00028
estimated CPU time 0.06 min
estimated wall time 0.02 min
writing file <hessian>.
The systematic shift of the HVF caused by the modification of the PES due to the biasing potential is subsequently removed approximately by individual frequency scaling, giving access to accurate thermostatistical contributions for general nonequilibrium geometries with low-level methods.
The desired target RMSD between the input and constrained optimized structure can be influenced by the $metadyn block of the xcontrol file.
$metadyn
rmsd=real
target RMSD between input and optimized structure (default: 0.10 Å)
Molecular Dyamics Simulations¶
In this chapter, all necessary information will be given in order to perform MD simulations with xTB. The adjustable parameters will be discussed and a guide to how to change them will be given.
Contents
General command-line control¶
There are two main possibilities how to evoke a MD simulation.
With the flag --omd geometry optimization will be performed
and this structure then will be used for the MD simulation, a loose
optimization level will be chosen.
> xtb coord --omd
By using the flag --md the MD simulation will be performed directly with the user given input structure.
> xtb coord --md
It is strongly recommended to start the MD simulation from an xTB optimized structure. Otherwise there may be instabilities during the MD and the equilibration will be severely hindered.
Parameters¶
In order to change the parameters of the MD simulation the $md block
in the input file has to be modified.
key
value
default
description
dump
real
50 fs
interval for trajectory printout
hmass
integer
4 times
mass of hydrogen atoms
nvt
boolean
true
perform simulation in NVT ensemble
restart
boolean
false
read velocities from
mdrestarttemp
real
298.15 K
thermostat temperature
time
real
50 ps
total run time of simulation
sccacc
real
2.0
accuracy of xTB calculation in dynamics
shake
integer
2
use SHAKE algorithm to constrain bonds
0 = off, 1 = X-H only, 2 = all bonds
step
real
4 fs
time step for propagation
velo
boolean
false
also write out velocities
The above default setting should look like below in your input file
$md
temp=298.15 # in K
time= 50.0 # in ps
dump= 50.0 # in fs
step= 4.0 # in fs
velo=false
nvt =true
hmass=4
shake=2
sccacc=2.0
$end
Important
For MD simulations with GFN-FF the time step must be reduced, for more information see section GFN-Force-Field (GFN-FF)
MD specific Files¶
After the xtb program has performed the desired MD simulation the trajectory of the structures can be found in xtb.trj.
Furthermore, files with the names scoord.* are generated. After every picosecond of simulation the structure at this point will be written into these files. After a successful completion of the MD simulation a xtbmdok file will be touched. The structure and velocities at the end of the simulation will be written into a mdrestart file.
Trajectory¶
The number of structures in the xtb.trj file depends on the dump variable and the propagation time step.
For practical purposes the two parameters are converted into a dump frequency n = (dump step/time step), e.g.,
a structure is written to the trajecotry equidistantly at every n-th propagation step.
Due to this conversion the total number of structures in the xtb.trj file might be slightly larger
than the expected (total runtime/dump step).
The same applies to the scoord.* files.
Restart¶
The mdrestart file can be used to restart an MD simulation. This can be very helpful for equilibration purposes.
In order to achive this, in the $md block the restart parameter has to be set to true.
> cat restart.inp
$md
restart=true
Example/Case study¶
To summarize the most important topics of this chapter we will perform an MD simulation of the ethane molecule with xTB.
Make sure that xtb is properly set up and you have the following files in your working directory
> cat coord
$coord
1.82409443250962 -0.02380488009596 0.17250251620479 c
4.68095348739630 -0.02380488009596 0.17250308312263 c
1.09744635742609 1.41159121722257 -1.12629926294082 h
1.09744579050825 0.38329239564274 2.06499275150500 h
1.09744635742609 -1.86629844212581 -0.42118612892243 h
5.40760175145245 1.81868868193389 0.76619172824984 h
5.40760212939767 -0.43090215583466 -1.71998734115020 h
5.40760175145245 -1.45920097741449 1.47130486226824 h
$end
> cat md.inp
$md
time=10
step=1
temp=500
shake=1
As you can see, we will run the simulation for 10 ps with a timestep of 1 fs at a temperature of 500 Kelvin. Furthermore, all hydrogen-containing bonds will be constrained using the SHAKE algorithm. To start the simulation we call xtb as follows
> xtb coord --input md.inp --omd
The program will start with performing a geometry optimization,
the optimized structure used to start the dynamic can be found
and inspected in xtbopt.coord.
In the file xtb.trj we can find our trajectory. We can analyze the structures now by displaying them in a molecular graphics editor (e.g., MOLDEN, VMD etc. ) or a trajectory analyzer (e.g. TRAVIS).
Meta-Dynamics Simulations¶
In this guide, all necessary information will be given in order to perform
meta-dynamics (MTD) simulations with the xtb program.
For the theory behind our MTD approach please refer to:
S. Grimme, Exploration of Chemical Compound, Conformer, and Reaction Space with Meta-Dynamics Simulations Based on Tight-Binding Quantum Chemical Calculations, J. Chem. Theory Comput., 2019, 155, 2847-2862. DOI: 10.1021/acs.jctc.9b00143 Publication Date (Web): April 3, 2019
Contents
From a practical point of view the application of meta-dynamics is quite similar to molecular-dynamic simulations. In MTD simulations a biasing potential given as a sum of Gaussian functions is additionally expressed. The root-mean-square deviation (RMSD) in Cartesian space is chosen as a metric for the collective variables.
All adjustable parameters will be discussed and a guide to how to change them will be given as well as an example.
General MTD Setup¶
For any MTD calculation a Detailed Input file is necessary to enter
the correct calculation mode. The basic parameters for dynamics are taken
from the $md block as described in the section regarding Molecular Dyamics Simulations.
The $metadyn data group has to be present in the input file.
All available instructions for this data group are shown here:
key
value
description
save
integer
maximal number of structures for rmsd criteria
kpush
real
scaling factor for rmsd criteria
alp
real
width of the gaussian potential used in the rmsd criteria
coord
file
external structure file to initialize rmsd criteria
atoms
list
atoms to include in the rmsd calculation (default: all)
To avoid accidental activation of the bias potential conservative default values
are chosen in the program. So you cannot simply use a commandline-only approach
to perform a MTD calculation. First of all you want to create a metadyn.inp
file with this content
$metadyn
save=10
kpush=1.0
alp=0.2
$end
You can start the metadynamic calculation now by using the --md commandline
flag as
> xtb --md --input metadyn.inp coord
By using the flag --metadyn integer, the number of saved structures may
also be entered via the commandline and need not to be present in the
detailed input:
> xtb --metadyn 10 --input metadyn.inp coord
MTD specific Files¶
After the xtb program has performed the desired MTD simulation the trajectory of the structures can be found in xtb.trj.
Furthermore, files with the names scoord.* are generated. After every picosecond of simulation the structure at this point
will be written into these files. After a successful completion of the MTD simulation a xtbmdok file will be touched.
The structure and velocities at the end of the simulation will be written into a mdrestart file.
Restart¶
The mdrestart file can be used to restart an MTD simulation. This can be very helpful for equilibration purposes.
In order to achive this, in the $md block the restart parameter has to be set to true.
> cat xcontrol
$md
restart=true
Example/Case study¶
To summarize the most important topics of this chapter we will perform an MTD simulation of the water dimer molecule with xTB.
Make sure that xtb is properly set up and you have the following files in your working directory
> cat coord
$coord
-3.41057596145012 0.01397950240733 -2.48858246259228 o
-4.61882519451466 -0.37951683073135 -3.80598534178089 h
-3.93472948277574 1.59474363012965 -1.77520048297923 h
-6.45960866143682 -1.52443579539520 -6.62024481959292 o
-5.26218381176973 -1.40667057754076 -7.97781013203256 h
-6.78373759577982 -3.28799737179945 -6.34039886662289 h
$end
> cat metadyn.inp
$md
time=10
step=1
temp=298
$end
$metadyn
atoms: 1-3
save=10
kpush=0.02
alp=1.2
$end
As you can see, we will run the MTD simulation for 10 ps with a timestep of 1 fs at a temperature of 298 Kelvin. For the meta-dynamics, only the structure of the first water molecule will be taken into account in the rmsd criteria. To start the simulation we call xtb as follows
> xtb --md --input metadyn.inp coord
The output for the example MTD simulation of the water dimer will look like this:
-------------------------------------------------
| Meta Dynamics |
-------------------------------------------------
trajectories on xtb.trj or xtb.trj.<n>
MD time /ps : 10.00
dt /fs : 1.00
SCC accuracy : 1.00
temperature /K : 298.00
max steps : 10000
block length (av.) : 5000
dumpstep(trj) /fs : 100.00 100
dumpstep(coords)/fs: 1000.00 1000
H atoms mass (amu) : 2
# deg. of freedom : 14
SHAKE on. # bonds : 4 all: T
Berendsen THERMOSTAT on
kpush : 0.020
alpha : 1.200
update : 10
time (ps) <Epot> Ekin <T> T Etot
0 0.00 0.00000 0.0198 0. 0. -10.10916
est. speed in wall clock h for 100 ps : 0.01
200 0.20 -10.09118 0.0116 559. 524. -10.12881
400 0.40 -10.11436 0.0105 454. 471. -10.13041
600 0.60 -10.12260 0.0070 431. 316. -10.13157
800 0.80 -10.12671 0.0071 412. 321. -10.13081
... ... ... ... ... ... ...
4800 4.80 -10.13763 0.0084 469. 379. -10.13198
block <Epot> / <T> : -10.13978 465. drift: 0.99D+02 Tbath : 298.
5000 5.00 -10.13775 0.0082 465. 368. -10.13253
5200 5.20 -10.13783 0.0129 469. 582. -10.12808
5400 5.40 -10.13794 0.0105 471. 474. -10.13014
5600 5.60 -10.13804 0.0090 470. 407. -10.13140
... ... ... ... ... ... ...
9800 9.80 -10.13918 0.0083 462. 376. -10.13258
average properties
Epot : -10.1392169717059
Epot (accurate SCC): -10.1402473210558
Ekin : 1.019492766065306E-002
Etot : -10.1290220440452
T : 459.900938472654
thermostating problem
normal exit of md()
In the file xtb.trj we can find our trajectory.
We can analyze the structures now by displaying them in a molecular graphics editor (e.g., MOLDEN, VMD etc. )
or a trajectory analyzer (e.g. TRAVIS).
Constrained MD/MTD simulations¶
As you may have noticed in the example given above by checking the file xtb.trj, the water dimer dissociates within
the MTD simulation due to the applied bias potential. If you run dynamics for systems that are non-covalently bound,
you may encounter this problem from time to time. To avoid dissociation you can try to confine the simulation in a sphere by
a repulsive potential. For further details check how to confine a cavity in Detailed Input.
To avoid dissociation of the water dimer by a logfermi potential, the input file has to be modified:
> cat metadyn.inp
$md
time=10
step=1
temp=298
$end
$metadyn
atoms: 1-3
save=10
kpush=0.02
alp=1.2
$end
$wall
potential=logfermi
sphere: auto, all
$end
To start the constrained MTD simulation we call xtb as follows:
> xtb --md --input metadyn.inp coord
If you now check the trajectory file, you will see that the water molecules do not separate.
Note
The wall potential does not only work for MD/MTD simulations. It may also be applied in the same manner for single point calculations and geometry optimizations.
Reaction Path Methods¶
Important
This guide refers to the meta-dynamics reaction path finder. While this approach is simpler and usually faster than nugded elastic band (NEB) methods or growing string methods (GSM) it might not be as reliable for more difficult reaction paths.
See the Growing String Method guide for details on alternative reaction path finders.
Setting up the Path Input¶
The meta-dynamics reaction path finder is based on a simple metadynamics bias potential adding a repulsive potential on the reactant structure and an attractive potential on the product structure. If the potential is chosen correctly a straight-forward geometry optimization should yield the reaction path between reactant and product.
The main difficulty lies in the choice of the correct repulsive and attractive potential to avoid artificial local minima that will stop the optimization. To overcome this issue the meta-dynamics reaction path finder will run several combinations of potential shapes to obtain the reaction path.
A usual invokation of the path finder is given here
xtb start.xyz --path end.xyz --input path.inp
For this guide we will use the GFN2-xTB since we want to form bonds.
If you want to use GFN-FF, keep in mind, that the GFN-FF can only break bonds, dissociation reactions will therefore usually work fine, while association reactions are likely to fail, as the topology is generated for the reactant geometry. If you want to model an association try to swap reactant and product and model the respective dissociation instead or use a quantum mechanical method like GFN2-xTB instead.
The recommended settings for running the pathfinder can be somewhat system dependent, a good starting point is this set of values:
$path
nrun=1
npoint=25
anopt=10
kpush=0.003
kpull=-0.015
ppull=0.05
alp=1.2
$end
Example Run¶
A possible input for a Diels-Alder reaction is given here. The starting structure for this example
15
C -1.05403119 -0.85921125 -1.07844148
O -0.74716995 -1.59204846 0.00037929
C 1.91999122 0.31825506 -0.65929558
C -1.56348463 0.34378897 -0.70923752
C -1.05432765 -0.85883374 1.07895685
C 1.92016161 0.31774885 0.65905212
C -1.56373749 0.34366980 0.70888173
H -0.86626022 -1.30691107 -2.03849048
H 2.21980037 -0.54462844 -1.23619995
H 1.61547946 1.18008308 -1.23636699
H -1.89753571 1.13638114 -1.35561033
H -0.86679445 -1.30614725 2.03907198
H 2.21960266 -0.54586684 1.23524723
H 1.61610877 1.17913244 1.23678680
H -1.89780281 1.13623322 1.35526633
The product structure given here
15
C -0.33650300 -0.52567500 -1.05221900
O -0.49920800 -1.44888700 0.00032300
C 1.08232400 0.03657400 -0.76729600
C -1.29917500 0.57935400 -0.66347200
C -0.33671300 -0.52527900 1.05252700
C 1.08262000 0.03575900 0.76715400
C -1.29967800 0.57933100 0.66328300
H -0.47204500 -0.99959700 -2.02194900
H 1.84062900 -0.63339500 -1.16910900
H 1.22478200 1.02637400 -1.19722100
H -1.79017300 1.24152200 -1.35666900
H -0.47213100 -0.99881000 2.02246200
H 1.84129300 -0.63425300 1.16825900
H 1.22479600 1.02528600 1.19777000
H -1.79081700 1.24169700 1.35615700
Running the calculation should yield an output similar to this
-------------------------------------------------
| P A T H |
| RMSD-Push/Pull Path Finder |
-------------------------------------------------
reading reference structures from end.xyz ...
reactant product RMSD : 1.010
initial k push/pull (in code xNat) : 0.003 -0.015
initial Gaussian width (1/Bohr) : 1.200
# refinement runs : 1
# of 'an'-optimization steps : 10
# optlevel : 0
degenerate system : F 0.260023 0.367379
24 # points, run 1 for k push/pull/alpha : 0.003 -0.015 1.200 prod-ed RMSD: 0.018
23 # points, run 2 for k push/pull/alpha : 0.003 -0.013 1.200 prod-ed RMSD: 0.017
path trials (see xtbpath_*.xyz), energies in kcal/mol
run 1 barrier: 116.09 dE: -25.06 product-end path RMSD: 0.018
run 2 barrier: 12.52 dE: -25.08 product-end path RMSD: 0.017
path 2 taken with 23 points.
screening points ...
start path on file xtbpath_0.xyz
refinement cycle 1
optimizing points 2 ...
optimizing points 10 ...
optimizing points 20 ...
forward barrier (kcal) : 12.420
backward barrier (kcal) : 37.497
reaction energy (kcal) : -25.076
opt. pull strength : 0.050
norm(g) at est. TS, point: 0.01615 11
terminated because max. # cycles reached
estimated TS on file xtbpath_ts.xyz
path data (pmode=approx. path mode):
point drms energy pmode ovlp pmode grad
2 0.000 -0.025 0.996 -0.00004
3 0.066 0.177 0.999 0.00032
4 0.134 0.570 0.999 0.00062
5 0.202 1.146 0.999 0.00092
6 0.269 1.984 0.999 0.00137
7 0.334 3.094 0.997 0.00179
8 0.400 4.629 0.995 0.00245
9 0.466 6.516 0.982 0.00303
10 0.532 8.988 0.900 0.00373
11 0.603 12.420 0.939 0.00374
12 0.700 -12.104 0.772 -0.01147
13 0.927 -17.963 0.806 -0.01343
14 0.974 -21.578 0.948 -0.00871
15 1.018 -23.406 0.612 -0.00549
16 1.053 -24.364 0.207 -0.00297
17 1.088 -24.348 -0.080 0.00006
18 1.117 -24.149 -0.414 0.00084
19 1.142 -24.574 -0.534 -0.00194
20 1.165 -24.941 -0.212 -0.00168
21 1.189 -24.865 -0.748 0.00043
22 1.208 -25.100 -0.450 -0.00123
23 1.228 -25.076 0.077 0.00031
The final transition state guess can be found in xtbpath_ts.xyz, depicted here:
Growing String Method¶
Note
gsm is not developed in our group but in the ZimmermanGroup, therefore this tutorial and the useage of GSM is without warranty of completness or correctness.
gsm is not able to communicate with xtb, therefore a fake orca output is created using the xtb values.
To run a gsm calculation, the following programs / files are needed.
gsm.orca in any valid path, e.g. your bin
inpfileq in the directory, where you want to execute your calculation
modified ograd in the directory, where you want to execute your calculation
tm2orca.py in any valid path, e.g. your bin
Those are distributed from our fork of gsm here for your convenience.
For further information and a detailed description on gsm, see ZimmermanGroup and their orca interface.
Input¶
gsm is a method to find a reaction path and a transition state. In the following, we are going to work with the Double-Ended Growing String Method (DE-GSM), therefore a converged start and end structure is needed. The atomic order needs to be the same in both files, otherwise the gsm calculation will not give the transition state you are looking for.
In your current working directory cwd/ you need to have the files inpfileq and ograd, and the directory scratch/. In scratch/, all files created and needed during the calculation are saved, but in the beginning, there is only one file in scratch/, named initial0000.xyz. The file initial0000.xyz contains the start and the end structure in any valid Xmol format. With the inpfileq the user is able to set specific parameters for the gsm calculation, whereas the ograd wraps xtb and converts input and output for gsm. This is necessary, as gsm can read orca output but not xtb output. To use gsm with xtb, we therefore have to fake an orca output, which is done using the tm2orca.py script.
> cd cwd/
> ls
inpfileq ograd* scratch/
Inversion¶
This example deals with the inversion of cyclohexane from the chair to the boat conformation. Firstly, you need a converged starting structure start.xyz. You therefore have to build your molecule using a smiles string, avogadro or any other graphical program of your choice. Afterwards you have to execute a quick geometry optimization (e.g. with xtb) and copy the obtained converged structure back in your cwd/.
> xtb unconverged.xyz --opt
> cp xtbopt.xyz ../start.xyz
Obviously, the xtb calculation can be done using all flags explained in this documentation, e.g. –chrg, –uhf, –alpb and so on.
The same has to be done with the end structure. It is advisable to take the optimized start structure and change, whatever you want to change, using a graphical program, which does not change your atomic order, e.g. avogadro, as a change in the atomic order will definitively cause problems during the DE-GSM calculation!
Before you can start the calculation, a couple of other things have to be done. First, you have to generate your initial0000.xyz.
> cat start.xyz end.xyz > scratch/initial0000.xyz
> cat scratch/initial0000.xyz
18
C 0.72407050811334 1.25235108200516 -0.24338094705465
C -0.72343762657313 1.25319617766380 0.23929059852918
C -1.44731174776017 -0.00012207898744 -0.24387881064420
C -0.72448059275055 -1.25351379257321 0.24067027167326
C 0.72302665800789 -1.25441395902634 -0.24200633751896
C 1.44695184726671 -0.00106936630608 0.24102971332150
H 0.74079379322633 1.27977999101331 -1.33568337236737
H 1.23911262989111 2.14407418287692 0.12103331256485
H -1.23773720847930 2.14497568327721 -0.12601425207736
H -0.74014360366626 1.28171032471934 1.33155904823478
H -2.47725186596728 0.00050340452584 0.12007291068245
H -1.47894487592394 -0.00071222738449 -1.33620018565333
H -0.74120355748858 -1.28080687484113 1.33297520098609
H -1.23953398541620 -2.14527362819323 -0.12363941525185
H 1.23731965319244 -2.14616191699557 0.12338823394548
H 0.73972201150389 -1.28305135703018 -1.33427294070718
H 1.47879051289637 -0.00048052377193 1.33334318895494
H 2.47682744992731 -0.00169512097196 -0.12311621761763
18
C 0.73801367871811 1.26986541848913 -0.29891956390957
C -0.72425034407001 1.23660126909089 0.13751131482082
C -1.44534047314084 -0.03177648038732 -0.35671028842475
C -0.51312926640361 -0.95386524177349 -1.13921033932034
C 0.73874270548611 -1.27320174695686 -0.32527750643084
C 1.46163460859193 0.00218599807452 0.14815613748902
H 0.80167461165837 1.37397900540374 -1.38290508569736
H 1.22823701649042 2.14109015941832 0.14110672721895
H -1.22954714616749 2.12895335124983 -0.23651035666162
H -0.75981821609326 1.27774751863575 1.22804091215143
H -1.84194534594910 -0.58465393222957 0.49789315375467
H -2.29332568018213 0.23757670740058 -0.98938629993452
H -1.03732116020641 -1.88207230826469 -1.37787118249708
H -0.23326413070136 -0.48637114937456 -2.08427188018927
H 0.44512664267991 -1.87161892139158 0.54024210888424
H 1.41101252131720 -1.88609677273023 -0.92920597460851
H 1.52271848431407 0.00555688995561 1.23838178865502
H 2.48432149365809 0.02132023538992 -0.23310366530028
Then you have to modify your inpfileq. Normally, all default values can be used, and you only have to care about the last two entries TS_FINAL_TYPE and NNODES. TS_FINAL_TYPE can be 0 or 1. 0 means no bond breaking and is used for this inversion, whereas you have to use 1 for a bond breaking. If you use the wrong setting here, so in this case 1 for the inversion of cyclohexane, gsm tries to break a bond leading to a wrong path. NNODES is the maximum number of nodes for the DE-GSM calculation and should be set to at least 15 for xtb.
TS_FINAL_TYPE 0 # 0=No bond breaking, 1=breaking of bond
NNODES 15 # including endpoints
Last, you have to modify the xtb call in ograd*. The $ofile.xyz as well as the –grad flag are necessary, but you can modify e.g. your charge or alpb flag. In the case of cyclohexane, the charge is 0 and for simplifications I just calculate it in gasphase, therefore no ALPB is used.
xtb $ofile.xyz --grad --chrg 0 > $ofile.xtbout
Now, you have done everything to start the calculation.
> gsm.orca
After the calculation, the two most important files are the reaction path in your cwd/, called stringfile.xyz0000, and the transition state in scratch/tsq0000.xyz, both in a valid Xmol format. The reaction path of the Inversion of cyclohexane can be seen below.
Inversion of cyclohexane¶
Energy diagram of the inversion of cyclohexane¶
Bond breaking¶
The next example is a simple Claisen rearrangement of an allyl vinyl ether and consequently includes a bond breaking and building. The initial0000.xyz is build as described above by writing the converged start and end structure one after the other.
> cat start.xyz end.xyz > scratch/initial0000.xyz
> cat scratch/initial0000.xyz
14
C 0.33830681 -0.40028145 0.06863012
C 0.10595161 -0.26718767 1.36421188
H 1.33077226 -0.61906183 -0.27493881
H -0.42216146 -0.28728678 -0.68244497
O -1.06599246 -0.01419187 2.00107453
H 0.89080386 -0.36692363 2.10223944
C -2.24339525 0.08535540 1.21865884
H -3.06296651 0.00347496 1.94095352
C -2.38810216 1.37002374 0.45318426
H -2.30704191 -0.76808842 0.53050462
H -3.21531691 1.36845744 -0.24273208
C -1.61866094 2.43160218 0.59926563
H -0.79697159 2.43969569 1.29630648
H -1.77723230 3.33005423 0.02997950
14
C 0.05083404 0.47756955 0.03067754
C 0.22099793 -0.53384083 1.12248949
H 1.00063556 0.99546491 -0.11008883
H -0.23550427 -0.01507412 -0.90051555
O -0.06214314 -1.70052772 1.01406801
H 0.61484477 -0.11647527 2.06863484
C -3.09105601 0.69502179 1.56213016
H -4.07672239 0.25168355 1.53446340
C -2.38605593 0.89986170 0.46164886
H -2.72406577 0.97143579 2.54163695
H -2.77578741 0.61350077 -0.51143129
C -1.01585926 1.51412664 0.44531292
H -0.76139644 1.92312285 1.42742393
H -0.99072867 2.32977240 -0.28155745
Next, the inpfileq is modified. As we are now dealing with a bond breaking, the TS_FINAL_TYPE has to be adapted. The NNODES is also changed to a higher value to give a more detailed reaction path. This is not necessary and was just done to play a bit with the settings.
TS_FINAL_TYPE 1 # 0=No bond breaking, 1=breaking of bond
NNODES 20 # including endpoints
At the end, the ograd* has to be modified. As Claisen rearrangements are often done in polar solvents, the calculcation was done using ALPB(water).
xtb $ofile.xyz --grad --chrg 0 --alpb h2o > $ofile.xtbout
tm2orca.py $basename
Now, the gsm calculation is done
> gsm.orca
The reaction path as well as the energy diagram are given below.
Reaction path of a claisen rearrangement¶
Energy diagram of a claisen reaction¶
Wrong atomic order¶
The following is an example that shows how important a proper atom order is. It deals with the same Claisen rearrangement as shown above, but with a different atom order in the start and end structure file, as shown below.
vimdiff of different atomic order in the start (left) and end (right) file¶
Except for the different atom order the same as above was done. Both structures are written to the initial0000.xyz in the scratch/* directory. In the inpfileq the TS_FINAL_TYPE is 1, and the NNODES is set to 20. The xtb call in ograd* is given below:
xtb $ofile.xyz --grad --chrg 0 --alpb h2o > $ofile.xtbout
Now gsm is just started as already shown.
> gsm.orca
The resulting path as well as the energy diagram is shown below.
Reaction path of a claisen rearrangement with wrong atom order¶
Example of an energy diagram of a wrong reaction path¶
Periodic Boundary Conditions¶
xtb is supposed to throw a lot of feature-not-implemented errors at
you as you try out the very recently added periodic boundary conditions.
You can make use of the C-API and the ASE calculator class to get around this
errors for now, but we promise to add more features and runtypes in the future.
Input Formats¶
We support Turbomole’s coordinate files in a riper compatible format.
It requires to have the $periodic information, one of $lattice or $cell
and, of course, a $coord data group present.
In contrast to Turbomole we want them all in one file,
so the file=<elsewhere> does not work with xtb.
A valid input for diamond is
$periodic 3
$cell angs
3.570 3.570 3.570 90 90 90
$coord angs
0.00000 0.00000 0.00000 C
0.89250 0.89250 0.89250 C
1.78500 1.78500 0.00000 C
2.67750 2.67750 0.89250 C
1.78500 0.00000 1.78500 C
2.67750 0.89250 2.67750 C
0.00000 1.78500 1.78500 C
0.89250 2.67750 2.67750 C
$end
or using different keywords and order like for calciumfluoride here
$coord frac
0.250000000 0.250000000 0.250000000 f
0.750000000 0.750000000 0.750000000 f
0.000000000 0.000000000 0.000000000 ca
$lattice angs
3.153833580 1.115048556 1.931320751
0.000000000 3.345145667 1.931320751
0.000000000 0.000000000 3.862641503
$periodic 3
$end
Note
we do not care if you $end your file or maybe even all your
data groups, since the parser politely ignores its presence.
While this format in principle is able to specify also 1D and 2D periodic
systems xtb does not support them right now.
Both Vasp 4 and Vasp 5 POSCAR and CONTCAR files are supported, but we require to have the information on the atomtypes present in the file. For details on the format refer to the documentation of Vasp.
Tip
You can use ase convert to bring your cif or fort.34 files
into Vasp format, as xtb currently cannot read them.
Geometry Optimizations¶
Note
feature implemented in version 6.2
To perform geometry optimizations with xtb on periodic systems we
recommend to use an input file like
$opt
engine=inertial
$end
Since the ANC optimizers do not support periodic boundary conditions right now, use the inertial relaxation procedure instead.
The optimization log is written in Vasp 5 POSCAR format and contains the current energy and gradient norm in the first (comment) line.
External Potentials and Embedding¶
xtb supports external electrostatic potentials for GFN1-xTB and GFN2-xTB.
Example: The Water Tetramer in Pieces¶
As input geometry for the QM half of the water cluster we use
$coord
-2.75237178376284 2.43247309226225 -0.01392519847964 O
-0.93157260886974 2.79621404458590 -0.01863384029005 H
-3.43820531288547 3.30583608421060 1.42134539425148 H
-2.43247309226225 -2.75237178376284 0.01392519847964 O
-2.79621404458590 -0.93157260886974 0.01863384029005 H
-3.30583608421060 -3.43820531288547 -1.42134539425148 H
$end
The setup will look somewhat similar to this
> ls
pcem.input water_4.coord water_4.pc
> cat pcem.input
$embedding
input=water_4.pc
$end
> xtb water_4.coord -I pcem.input
...
The file water_4.pc contains the partial charges and its positions as
6
-0.69645733 2.75237178376284 -2.43247309226225 -0.01392519847964 O
0.36031084 0.93157260886974 -2.79621404458590 -0.01863384029005 H
0.33614649 3.43820531288547 -3.30583608421060 1.42134539425148 H
-0.69645733 2.43247309226225 2.75237178376284 0.01392519847964 O
0.36031084 2.79621404458590 0.93157260886974 0.01863384029005 H
0.33614649 3.30583608421060 3.43820531288547 -1.42134539425148 H
The first column contains the partial charge, the second to fourth columns
contain the cartesian coordinates in Bohr (or in Ångström if interface=orca
is used in the input file).
The fifth column is optional, but can contain, like here, element symbols
to specify the chemical hardnesses of the partial charges.
Note that we are not using real point charges here but a damped Coulomb interaction
consistent to the electrostatic interactions used in the respective
xTB Hamiltonian.
The read in point charges are shown in the setup block of the SCC as
... skip ...
-------------------------------------------------
| Self-Consistent Charge Iterations |
-------------------------------------------------
...................................................
: SETUP :
:.................................................:
: # basis functions 12 :
: # atomic orbitals 12 :
: # shells 8 :
: # electrons 16 :
: max. iterations 250 :
: Hamiltonian GFN2-xTB :
: restarted? false :
: GBSA solvation false :
: PC potential true :
: -> # point charges 6 :
: -> sum of PC 0.0000000 e :
: electronic temp. 300.0000000 K :
: accuracy 1.0000000 :
: -> integral cutoff 0.2500000E+02 :
: -> integral neglect 0.1000000E-07 :
: -> SCF convergence 0.1000000E-05 Eh :
: -> wf. convergence 0.1000000E-03 e :
: Broyden damping 0.4000000 :
...................................................
iter E dE RMSdq gap omega full diag
1 -10.2141283 -0.102141E+02 0.418E+00 13.25 0.0 T
2 -10.2169842 -0.285597E-02 0.241E+00 13.15 1.0 T
3 -10.2175075 -0.523314E-03 0.392E-01 12.35 1.0 T
4 -10.2176392 -0.131616E-03 0.871E-02 12.57 1.0 T
5 -10.2176471 -0.790990E-05 0.417E-02 12.50 1.0 T
6 -10.2176488 -0.172257E-05 0.237E-03 12.52 17.3 T
7 -10.2176488 -0.524712E-08 0.835E-04 12.52 48.9 T
8 -10.2176488 0.134836E-09 0.623E-04 12.52 65.5 T
*** convergence criteria satisfied after 8 iterations ***
... skip ...
:::::::::::::::::::::::::::::::::::::::::::::::::::::
:: SUMMARY ::
:::::::::::::::::::::::::::::::::::::::::::::::::::::
:: total energy -10.155934019173 Eh ::
:: gradient norm 0.024959693967 Eh/a0 ::
:: HOMO-LUMO gap 12.520985724021 eV ::
::.................................................::
:: SCC energy -10.217648797540 Eh ::
:: -> isotropic ES 0.066792092832 Eh ::
:: -> anisotropic ES -0.002669047466 Eh ::
:: -> anisotropic XC -0.001310421597 Eh ::
:: -> dispersion -0.000808230531 Eh ::
:: repulsion energy 0.061714760838 Eh ::
:: add. restraining 0.000000000000 Eh ::
:::::::::::::::::::::::::::::::::::::::::::::::::::::
... skip ...
To obtain point charge like behaviour for the partial charges the chemical
hardness can be set to a large value. This can be done by specifying the chemical
hardnesses in the fifth column instead of giving an element symbol.
For this setup the water_4.pc would look like
6
-0.69645733 2.75237178376284 -2.43247309226225 -0.01392519847964 99
0.36031084 0.93157260886974 -2.79621404458590 -0.01863384029005 99
0.33614649 3.43820531288547 -3.30583608421060 1.42134539425148 99
-0.69645733 2.43247309226225 2.75237178376284 0.01392519847964 99
0.36031084 2.79621404458590 0.93157260886974 0.01863384029005 99
0.33614649 3.30583608421060 3.43820531288547 -1.42134539425148 99
GFN-Force-Field (GFN-FF)¶
Contents
Introducing GFN-FF¶
GFN-FF is a completely automated partially polarizable generic force-field for the accurate description of
structures and dynamics of large molecules across the periodic table. This method combines force-field speed
with almost quantum mechanical accuracy.
The main publication for GFN-FF can be found at: Angewandte Chemie.
Theoretical background¶
The latest progress in the field of semi empirical methods, regarding the evolution of GFN1, GFN2 and GFN0-xTB, inspired the development of a generic force-field. The main focus of this GFN force-field (GFN-FF) is directed towards the description of bio-macromolecular systems such as (metallo-) proteins, supramolecular assemblies and metal-organic frameworks. It is intended for the usage as a versatile tool for drug design in life sciences and structure screening in various fields of chemistry. Therefore, GFN-FF introduces an approximation to the remaining quantum mechanics in GFN0-xTB by replacing the extended Hückel theory by molecular mechanical bond strech, bond angle angle and torsion angle terms for the description of covalent bonds. To remain accurate in the description of conjugated systems, GFN-FF retains an iterative Hückel scheme for a selected set of atoms. The resulting bond orders obtained by a Hückel calculation have an influence on force constants and energy relevant parameters of the system. To yield accurate results the FF parameters are fitted to reproduce B97-3c minimum geometries and frequencies. Thereby a strictly global and element specific parameter strategy is applied and no element pair specific parameters are employed. Special attention is paid to the simple application. As input only Cartesian coordinates and elemental composition are required from which fully automatically all potential energy terms are constructed. The total GFN-FF energy expression is given by
where \(E_{cov}\) refers to the bonded FF energy and \(E_{NCI}\) describes the intra- and intermolecular noncovalent interactions. In the covalent part interactions are described by asymptotically correct (dissociative) bonding, angular and torsional terms. Repulsive terms are added for bonded and non-bonded interactions separately. Additionally a three-body correction to the nuclear repulsion is added, that extends beyond the sum of pair-wise interactions.
In the noncovalent part, electrostatic interactions are described by an electronegativity equilibrium (EEQ) model. It is employed to calculate the isotropic electrostatic energy and atomic partial charges. Overall GFN-FF uses two sets of EEQ charges. One set depends on the standard geometry, whereas another set of charges is exclusively topology based, introducing partial polarizability to the FF method. Dispersion interactions are taken into account by a topology based version of the D4 scheme, in which the dispersion coefficients are scaled by atomic charges instead of atomic polarizabilities. For the description of hydrogen and halogen bonds additional charge scaled H- and X- bond corrections are applied to yield the right binding motifs.
GFN-FF reaches quadratic scaling in terms of energy and gradient calculation, whereas all GFN-xTB methods show cubic scaling with respect to the number of atoms. It is the computationally most efficient member of the GFN family.
How to use it¶
GFN-FF is implemented in the xtb program. It extends the portfolio of different GFN parametrizations by a non-electronic variant. GFN-FF is applied with the keyword --gfnff as shown in the example below.
> xtb --gfnff <geometry> [options]
Thus, the usage is in line with its semiempirical QM siblings and (almost) the same options are available. Only the request of electronic structure properties will be ignored, since those are not available at the force-field level of theory. With GFN-FF you can perform single point calculations, geometry optimizations, frequency calculations and molecular dynamics simulations, just to mention the most prominent run types. A GFN-FF calculation is indicated in the output by:
-------------------------------------------------
| G F N - F F |
| A general generic force-field |
| Version 1.0.1 |
-------------------------------------------------
The topology file¶
GFN-FF generates a topology file named gfnff_topo automatically upon first use on an input structure. This file saves system specific parameters and derived force constants as well as the entire topological information. If the force-field calculation is repeated, the topology file is read.
GFN-FF topology read from file successfully!
Depending on the system size, this speeds up you the overall computation time If large structural changes are applied to the structure, the topology file should better be deleted. The next calculation will generate a new one, according to the modified structure. If parameters are changes in the code, the topology file should also be deleted, as the old parameters are also saved there.
GFN-FF specific settings¶
xtb is a semiempirical extended tight-binding program package and its default values are chosen to yield robust and accurate results for all GFN-xTB methods. GFN-FF represents the first non-electronic variant and thus it should come as no surprise, that some of the default values do not work with a generic force-field. Settings that deviate from the defaults are discussed below.
Parallelisation¶
The xtb program uses OMP parallelisation. To calculate larger systems an appropriate OMP stacksize must be provided. Since the system size may easily exceed 5000 atoms in force-field calculations, a large number should be chosen. Otherwise you may encounter a segmentation fault. For 5000 atoms you may choose:
> export OMP_STACKSIZE=5G
As a rule of thumb, add 1G for every additional 1000 atoms.
MD Simulations¶
For molecular dynamics simulations, the default time step of 4 ps is not stable in GFN-FF. Below you can find our recommended settings for a stable MD run.
$md
step=2.0
hmass=4.0
shake=0
$end
GFN-FF specific input¶
xtb accepts various input formats. Especially the possibility to directly read pdb files as input might be something you want to use in combination with GFN-FF. If the pdb file includes charge information, xtb reads this information, determines the overall charge of the system automatically and applies this charge constrain per residue. There is no need to further specify the total charge of the system. The following output is generated.
charge from pdb residues: <integer>
Use of additional charge information¶
In GFN-FF the computed atomic charges from the EEQ model may be improved by constrains if additional information about the charge distribution in the system is known. There are two further ways to incorporate this information besides using a pdb file. If the system consists of more than one NCI fragment, the charges per fragment can be written by the user into a specific file
(named .CHRG) and will be constrained accordingly in the EEQ model, thus preventing artificial charge transfer between the NCI fragments. If a GFN-xTB calculation is performed in advance, the written file charges is read by the program and the corresponding QM charges are used to constrain the values on the molecular fragments.
2D to 3D structure converter¶
xtb feaetures a 2D to 3D structure converter for sdf files. If a two-dimensional sdf file input is passed to xtb and a GFN2-xTB single point calculation is requested, it will automatically perform a combination of GFN-FF optimization and molecular dynamics steps to generate a three dimensional structure, on which the GFN2-xtB calculation is performed.
> xtb 2d_input.sdf --gfn 2 --sp
The keyword --gfnff is not needed here. The start of the structure conversion is indicated in the output by,
-------------------------------------------------
| 2D => 3D |
| A structure converter based on |
| G F N - F F |
-------------------------------------------------
and the successful conversion is confirmed by:
-------------------------------------------------
| 2D => 3D conversion done! |
-------------------------------------------------
converted geometry written to: gfnff_convert.sdf
C API to the extended tight binding program¶
The xtb program can included in other application by its
C application programmable interface (API) for all languages that
cannot access the Fortran modules directly.
The API declarations are given in xtb.h
Important
The C API is considered stable with version 6.3.0 and will be kept compatible to following versions.
Previous experimental API versions from the 6.2 series are deprecated.
The C side has to work with four different Fortran objects which are allocated and deallocated on the Fortran side and only provided as opaque data pointer.
Generally the first set for every API call is to construct a
calculation environment xtb_TEnvironment, which handles the input
and output streams and the error log.
The API will not perform any calculation if a null pointer is passed
instead of the environment and fail silently.
Note that once the environment has caught on an error all further
API calls will fail unless the environment is freed again and the
error has been handled.
xtb provides a persistent environment as well which is handled
entirely by the API. Producing an error for this environment is
consider fatal and will halt the program (usually via drastic means,
i.e., without giving the caller a way to react).
This case is always considered a bug in the API and should be reported.
The input data for the calculation is generated as molecular
structure data xtb_TMolecule. Note that the number of atoms,
the atomic number, the boundary conditions, total charge and
multiplicity are immutable and require to reconstruct the object.
Cartesian coordinates and lattice parameters are provided in Bohr
and can be updated after the object has been constructed.
Both the update and the constructor will fail on invalid input,
which are to close interatomic distances or atomic number outside of
the range 1 to 118 (while individual methods might impose additional
constraints).
The actual calculation can be performed with a single point
calculator xtb_TCalculator which must be loaded with a particular
parametrisation before it can be used for a calculation.
GFN2-xTB and GFN1-xTB can savely load their parametrisation without
a parameter file. For the experimental GFN0-xTB a parameter file
is required in the XTBPATH or must be provided by the API.
The GFN-FF can also provide its own parameters internally but
API support is still experimental.
Finally, the calculation results are stored in the xtb_TResults
object which can also be used to restart calculations from previous
runs (e.g. after updating coordinates).
The calculation results can be queried for properties they will
return in error in case the property is not available.
Passing calculation results from one calculator to another will
usually result in dimension missmatches, it is recommended to
reconstruct the results object for this purpose.
Generally, the API tries to be particular flexible in this case
and will try to reallocate the individual components as necessary.
Note that this can fail in particular if the total charge or
multiplicity of the molecular structure has changed.
A simple example program to obtain the total energy from a GFN2-xTB calculation is given here.
#include "xtb.h"
int
main (int argc, char** argv)
{
int const natoms = 7;
int const attyp[7] = {6,6,6,1,1,1,1};
double const charge = 0.0;
int const uhf = 0;
double const coord[3*7] =
{0.00000000000000, 0.00000000000000,-1.79755622305860,
0.00000000000000, 0.00000000000000, 0.95338756106749,
0.00000000000000, 0.00000000000000, 3.22281255790261,
-0.96412815539807,-1.66991895015711,-2.53624948351102,
-0.96412815539807, 1.66991895015711,-2.53624948351102,
1.92825631079613, 0.00000000000000,-2.53624948351102,
0.00000000000000, 0.00000000000000, 5.23010455462158};
/*
* All objects except for the molecular structure can be
* constructued without other objects present.
*
* The construction of the molecular structure locks the
* number of atoms, atomic number, total charge, multiplicity
* and boundary conditions.
**/
xtb_TEnvironment env = xtb_newEnvironment();
xtb_TCalculator calc = xtb_newCalculator();
xtb_TResults res = xtb_newResults();
xtb_TMolecule mol = xtb_newMolecule(
env, &natoms, attyp, coord, &charge, &uhf, NULL, NULL);
if (xtb_checkEnvironment(env)) {
xtb_showEnvironment(env, NULL);
return 1;
}
/*
* Apply changes to the environment which will be respected
* in all further API calls.
**/
xtb_setVerbosity(env, XTB_VERBOSITY_FULL);
if (xtb_checkEnvironment(env)) {
xtb_showEnvironment(env, NULL);
return 1;
}
/*
* Load a parametrisation, the last entry is a char* which can
* be used to provide a particular parameter file.
*
* Otherwise the XTBPATH environment variable is used to find
* parameter files.
*
* The calculator has to be reconstructed if the molecular
* structure is reconstructed.
**/
xtb_loadGFN2xTB(env, mol, calc, NULL);
if (xtb_checkEnvironment(env)) {
xtb_showEnvironment(env, NULL);
return 1;
}
/*
* Actual calculation, will populate the results object,
* the API can raise errors on failed SCF convergence or other
* numerical problems.
*
* Not supported boundary conditions are usually raised here.
**/
xtb_singlepoint(env, mol, calc, res);
if (xtb_checkEnvironment(env)) {
xtb_showEnvironment(env, NULL);
return 1;
}
/*
* Query the environment for properties, an error in the environment
* is not considered blocking for this calls and allows to query
* for multiple entries before handling possible errors
**/
xtb_getEnergy(env, res, &energy);
if (xtb_checkEnvironment(env)) {
xtb_showEnvironment(env, NULL);
return 1;
}
/*
* deconstructor will deallocate the objects and overwrite the
* pointer with NULL
**/
xtb_delResults(&res);
xtb_delCalculator(&calc);
xtb_delMolecule(&mol);
xtb_delEnvironment(&env);
return 0;
}
The header additionally defines macros for the version of the xtb API
to guard usage of API functionalities introduced in particular versions.
Python Integration for the xtb API¶
The xtb program does not provide a Python API on its own anymore,
it is now maintained in the xtb-python project.
The xtb-python project is hosted on GitHub.
The documention of the Python API can be found here.
Info Submodule¶
Note
This feature is only present in version 6.3 and newer
The info submodule allows to acquire information about the geometry as it
would be processed in a full xtb run, but without actually performing
a calculation.
The info submodule is invoked by
xtb info <geometry> [geometry] ...
and can handle multiple (read several thousand) input files sequentially.
In the normal run mode, with one input file, the info submodule will show
the number of atoms found, the identifier map and geometry specific information
as printed in the property printout.
These information can be used to verify xtb will correctly read the input
structure, in case of errors the info submodule will return with a non-zero
exit code.
The identifier map printed can be used in the detailed input to select certain group of atoms and is printed to show the found species and mapping in the input file
ID Z sym. atoms
1 6 C 1, 6-7, 13, 14
2 7 N 2, 4, 9, 12
3 6 C* 3, 10
4 8 18O 8
5 8 O 11
6 1 D 15-17
7 1 H 18-24
In batch mode, with multiple input files, the info submodule will generate additional diagnostics regarding the input files
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Processed 2474 individual inputs
11/2474 inputs failed info check( 0.4%)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
An summary of the errors will be found in the standard output when the file was processed, in case an error is encounter the info submodule will return with a non-zero exit code. Processing is not aborted due to errors. This can be used to validate structures before performing actual calculations.
Thermo Submodule¶
Note
This feature is only present in version 6.3 and newer
The thermo submodule allows to evaluate thermodynamic functions from data produced
in previous calculations, generally the results are equivalent to the ones
produced in a frequency calculation in xtb.
To run the thermo submodule use
xtb thermo [options] <geometry> [hessian]
The geometry can be any format accepted by xtb, while the hessian format
depends on the options passed to the thermo submodule.
It defaults to the non-massweigthed, projected Turbomole hessian data group.
Possible options are:
- --sthr REAL
Rotor cutoff for RRHO partition function in rcm
- --temp REAL
Temperature for thermodynamic functions in K, takes a comma separated list of temperatures
- --turbomole
Read a Turbomole Hessian file, use this only when $nomw is not present in control
- –dftb+
Read a DFTB+ hessian.out file, projection will be performed automatically
An example calculation is given here, reevaluating at a different rotor cutoff for multiple temperatures
xtb benzene.xyz --namespace benzene --ohess
...
xtb thermo --sthr 100 --temp 50,100,150,200,250,300 benzene.xtbopt.xyz benzene.hessian
...
Molecule has the following symmetry elements: (i) (C6) (C3) 7*(C2) (S6) (S3) 7*(sigma)
It seems to be the D6h point group
d6h symmetry found (for desy threshold: 0.10E+00) used in thermo
...
T/K H(0)-H(T)+PV H(T)/Eh T*S/Eh G(T)/Eh
------------------------------------------------------------------------
50.00 0.633464E-03 0.981387E-01 0.362609E-02 0.945126E-01
100.00 0.128528E-02 0.987905E-01 0.815319E-02 0.906373E-01
150.00 0.203561E-02 0.995409E-01 0.131373E-01 0.864036E-01
200.00 0.296494E-02 0.100470E+00 0.185801E-01 0.818901E-01
250.00 0.413423E-02 0.101639E+00 0.245239E-01 0.771156E-01
300.00 0.558192E-02 0.103087E+00 0.310070E-01 0.720801E-01 (used)
------------------------------------------------------------------------
...
Topology Submodule¶
Note
This feature is only present in version 6.3 and newer
The topology submodule allows to create a GFN-FF topology from a geometry input, which can be used to restart a calculation with the GFN-FF without having to perform a costly reevaluation of the force field topology
To start the generation use
xtb topo [--namspace <name>] <geometry>
If you want to use a particular namespace in the calculation later include
the namespace flag.
Note that even if you want to perform several GFN-FF calculation on different
namespaces, generate the topology file without a namespace is recommend,
as xtb will first search the local namespace and than fall back to the
default file name to finding the generated topology file.
Important
The force field generation step is a cubic scaling step as it requires an all pair shortest path (APSP) algorithm for generating the topological charges and for the diagonalization of the Hückel matrices for the torsion potentials, which can take, depending on the system of interest a significant portion of computation time.
The generated file will be named gfnff_topo or <name>.gfnff_topo and
can become quite large.
Introduction to CREST¶
Contents
What is CREST ?¶
CREST is an utility/driver program for the xtb program.
Originally it was designed as conformer sampling program, hence the abbreviation Conformer–Rotamer Ensemble Sampling Tool,
but now offers also some utility functions for calculations with the GFNn–xTB methods.
Generally the program functions as an IO based OMP scheduler (i.e., calculations are performed by the xtb program) and tool for the creation and analysation of structure ensembles.
The key procedure implemented in CREST is a conformational search workflow abbreviated as iMTD-GC.
The iMTD-GC workflow generates conformer/rotamer ensembles (CREs) by extensive metadynamic sampling (MTD) based on, with an additional genetic z-matrix crossing (GC) step at the end.
Other standalone functionalities that are included in CREST are parallel optimization and screening functions for GFNn–xTB,
the function to sort (e.g. for NMR equivalencies) externally created ensembles, and some automated procedures for the protonation, deprotonation and tautomerization of structures.
The main publication for the CREST program can be found at Phys. Chem. Chem. Phys., 2020, 22, 7169-7192.
Conformers and Rotamers¶
The thermally accessible ensemble of minimum-energy structures generally consists of conformers as well as rotamers, and hence can be called a conformer/rotamer ensemble (CRE). Many physical observables are obtained as time average over the different low energy conformations of a molecule. Hence, in computational chemistry, it can be important to perform calculations on the favored conformation or an ensemble of conformations. Some examples for macroscopic observables that are depending on the conformation are pKa values, CD spectra, NMR spectra, IR spectra, etc.. While calculations have generally only to be performed for different conformers (each having a distinct energy minimum, see figure below), rotamers can become important, e.g., for the calculation of NMR spectra where they represent the rapid (sub-experiment time scale) nuclei interchange leading to an average of NMR parameters.
Rotamers also contribute substantially to the molecular entropy and the completeness of the overall CRE. This can be assessed by a maximized entropy \(S_{CR}\) according to the standard thermodynamic expressions
where \(R\) is the molar gas constant and the sum runs over all populations \(p_i\) of all species with energy \(\Delta E_i\) at temperature \(T\), given as
The ensemble entropy \(S_{CR}\) is also linked to the ensemble free energy (at \(T =298\) K) \(G_{CR}=H-TS_{CR}\), which has to be minimized for a complete CRE.
In practice we use three descriptors to distinguish between conformers and rotamers: The energy, the rotational constant of the molecule and the RMSD between two molecules. If two structures have completely different energies they are conformers. If they have the same energy (within a chosen threshold) they could be either two different conformers with similar energies, two rotamers of the same molecule or a duplicate of the same rotamer. In the first case (two conformers with similar energies) the RMSD will be high and the rotational constant will be different. For two rotamers the RMSD will be high, but the rotational constant is the same (within a chosen threshold). Enantiomers (mirror image molecules) are a special case of rotamers matching the same criterium. Only for duplicates of the same rotamer (that have to be sorted out) the RMSD,the rotational constants, and the energies will be the same.
Conformational Search Algorithms¶
iMTD-GC Algorithm¶
The iMTD-GC workflow was designed to find low lying conformers more efficiently and more safely than the older MF-MD-GC algorithm (first algorithm in the original version of the program). Furthermore this new algorithm is more robust and generally applicable than more complicated schemes since it does not require any pre-definition of special system coordinates. iMTD-GC is rooted in the basic idea to combine GFNn–xTB calculations with root-mean-square-deviation (RMSD) based meta-dynamics (see section Meta-Dynamics Simulations). In practice a history-dependent biasing potential is applied, where the collective variables (CVs) for the meta-dynamics are previous minima on the PES, expressed as RMSD between the structures. The biasing contribution is given by Gaussian-type potential as
where the RMSD entera as collective variables \(\Delta_i\), \(n\) is the number of reference structures, \(k_i\) are the pushing strengths and the parameter \(\alpha\) determines the potentials’ shape. From this energy expression atomic forces are derived that enter as additional forces in the MTD simulations (in the context of meta-dynamics also sometimes refered to as guiding forces). Since the addition of each bias Gaussian drives the structure further away from previous geometries this allows otherwise unlikely high-barrier crossings where all atoms collectively explore huge regions of the potential energy surface.
Genetic Z-matrix crossing (GC) is related to the concept of genetic algorithms in such that structural elements present only in already generated structures are projected onto a reference to create new structures. By repeating the crossing procedures structural elements that appear more frequently would be inherited more often, being responsible for the ‘genetic’ character of this approach. Internal (Z-matrix, \(R\)) coordinates are employed and a new structure is generated by taking the differences to the reference \(R_{ref}\) over all internal coordinates (i.e., bond length, bond angles, an dihedral angles) according to
where \(R_i\) and \(R_j\) label the pairs and \(R_{new}\) is the generated new structure, which is subjected to a full geometry optimization. In this way, structural differences, e.g. a methyl group rotation, relative to \(R_{ref}\) present only in \(R_i\) and \(R_j\) are combined in the resulting new conformer/rotamer. The ensemble can be improved regarding the rotamers efficiently by the Z-matrix crossing. This effect is best visible for acyclic chains with a number of rotateable bonds, e.g., alkanes, but in principle it also works for more complicated cases, such as macrocyclic systems.
In practice the MTD simulation length is determined automatically by a flexibility measure of the molecule (typically \(t = 0.3-0.4 \times N\) ps per MTD). Several independent MTDs (at 300 K) are performed with different setings for \(\alpha\) (in Bohr\(^{-1}\)) and \(k_i/N\) (in \(mE_h\)). This has to be done since each molecule in principle requires a unique set of optimal \(\alpha\) and \(k\) and thus a variety of parameters ensures that the algorithm is perfroming well for all types of molecules. The snapshots are geometry optimized in a multi-level, three-step-filtering procedure by firstly applying two loose threshold settings followed by very tightly converged optimization and energy windows of 15, 10, and 6 kcal/mol, respectively. After the second step of this filtering also some short regular MD simulations are performed on the 6 lowermost conformers (at different temperatures 400 and 500 K), which is done to A) get rotamers and B) more extensively sample around these minima on the PSE ( i.e., find low-barrier conformers missed by the high-energy MTD treatment). In the last step the GC procedure is performed to further complete the CRE. The number of generated structures in this step is limited to \(min(3000,t\times50)\) in order to limit the computational cost. Furthermore a two-step-filtering procedure is used to optimize the generated geometries, similar to the three-step-filtering before.
The algorithm is iterative, i.e., if a new lower conformer is found at any point during the sampling the procedure is restarted with this conformer as an input. All CREs that are found within the iterations are included in the conformer/rotamer ranking process. The iMTD-GC worflow is outlined graphically in the figure below.
iMTD-sMTD and extended entropy calculations¶
Following CREST version 2.11 a new variant of the previous algorithm is introduced, called iMTD-sMTD.
The important new part of this algorithm are socalled static metadynamics simulations (sMTD), which are
practically more similar to umbrella sampling or basing-hopping algorithms.
Here, in each sMTD previously found conformers are added via \(V_{bias}\) as a global potential and,
opposed to the iMTD workflow, are not updated with new structures during the simulation.
Several iterations of sMTD are executed until convergence is achived with regards to the ensemble entropy
and number of conformers in the ensemble. After each sMTD iteration new bias structures for the potential are
identified using a PCA and k-Means ensemble clustering approach with dihedral angles as descriptors.
The iMTD-sMTD workflow is outlined in the figure below.
This algorithm can also be used not only for ensemble generation, but also provides the capability to determine a converged conformational entropy. After convergence this requires only two additional steps (outlined as the gray boxes in the figure), which are an extrapolation of the entropy based on the iterations of sMTD-iMTD and an averaged thermostatistical contribution \(\overline{S}_{msRRHO}\).
Note
The iMTD-sMTD workflow is more costly than iMTD-GC and hence NOT the default runtype of CREST.
The workflow can be used for conformational searches with the command --v4 or for entropy
calculations with the keyword --entropy.
CREST Versions and Changelog¶
Recent binaries can be found on GitHub (Linux operating systems only).
Note
Release candidates and beta versions are not listed here.
- Version 2.11 (1. Feb. 2020)
Code cleanup (pt. 2)
Moved
crestsource code to the repositoryRewritten ensemble sorting routine CREGEN
Connectivity/topology checks in CREGEN (can be turned off with
--notopo)Optional PCA and k-Means clustering after sorting (
--cluster <number>)Multiple smaller tools and improvements implemented
Updated input reader for Turbomole coord, .xyz and 3D .sdf (V2000,V3000) formats
Turned off
zsortdefault input sorting of coordinatesEnabled
--alpbusage (new implicit solvation model inxtb)Reduced creation of files during optimizations
Dedicated ensemble entropy (
--entropy) mode and iMTD-sMTD workflow (--v4)
- Version 2.10 (20th Apr. 2020)
Major code cleanup (pt. 1)
Moved
crestfromxtbto its own repositoryProper
SIGTERMandSIGINThandling implementedBugfix: Repaired integer overflow in ensemble sorting routine
Reduced memory consumption in ensemble sorting
Improved efficiency of ensemble sorting (for large ensembles)
Implemented automatic bond length constraint (
-cbonds)
- Version 2.9 (19th Feb. 2020)
Version consistent with main publication at PCCP
Literature references added, can be shown with
--cite
- Version 2.8.1
Minor bug fixes e.g. in
-scratch,-gbsaproperty mode now distinguished between
hessandohessGFN-FF interface (requires xtb 6.3 or newer)
- Version 2.8
Automated geometry optimization prior to calculations
New flags
-dry,-scratch,-cinp,--constrain,-subrmsdInitial framework for “property” mode (
-prop)
CREST command line arguments¶
Contents
CREST is usually invoked via commandline, and requires only a coordinate input file.
The program supports the TURBOMOLE coordinates (coord, Bohr), Xmol (*.xyz, Angstroem)
or 3d SDF (V2000,V3000) formats and can be called via
> crest [INPUT] [OPTIONS]
If no file is given as [INPUT], then CREST automatically searches for a file called coord
in the TURBOMOLE format. Either must be present. The different [OPTIONS] are listed below and refer
to Version 2.11 of the CREST code. [DEFAULT] options do not need to be specified explicitly.
General and techincal options¶
- flag
-h,-help- description
Print a overview of most avialable options (i.e., this site)
- flag
--version- description
Print only the program header and disclaimer.
- flag
--cite- description
Print the most relevant citations.
- flag
--xnam BIN- description
Specify the name (and path) of the
xtbbinary that sould be used as BIN. The[DEFAULT]is xtb.- flag
--niceprint- description
In-line progress bar printout for optimizations.
- flag
--scratch <DIR>- description
Performs the entire calculation in the specified
<DIR>. If<DIR>is not existing it will be created.- flag
--T <INT>- description
Specify the number of CPU threads
<INT>that shall be used.CRESTautomatically adjusts the number of processes according to this variable in each step, in order to achieve optimal parallelization of the calculations.- flag
--dry- description
Perfrom a “dry” run, i.e., nothing is actually done but instead an overview of the settings that would be applied in the calculation is given.
Runtypes¶
Several different applications are availabile within the CREST program.
The most important usage are the two different conformational search algorithms MF-MD-GC and iMTD-GC,
but there are also some smaller utility tools that can be used, such as an CRE sorting function (CREGEN),
or a standalone z-martix sorting function (ZSORT).
The different runtypes are:
- MF-MD-GC algorithm (outdated)
- flag
--v1- description
First generation of the GFNn-xTB driven conformational search algorithm, consisting out of mode following, molecular dynamics sampling and genetic structure crossing.
- MTD-GC algorithm (outdated)
- flag
--v2- description
Second generation of the GFNn-xTB driven conformational search algorithm, consisting out of a meta-dynamics approach and genetic structure crossing.
- iMTD-GC algorithm
[DEFAULT] - flag
--v2i, --v3- description
Iterative version of the MTD-GC workflow, which is the default runtype of
CREST.
- iMTD-sMTD algorithm
- flag
--v4- description
Iterative workflow, making use of static metadynmics simulations.
- Conformational entropy algorithm
- flag
--entropy- description
Specialized version of the iMTD-sMTD workflow, specialized in the calculation of conformational entropy.
Ensemble sorting¶
- CREGEN ensemble sorting tool for standalone use
- flag
--cregen <FILE>- description
Tool to sort a given ensemble
<FILE>according to energy, atomic RMSD and rotational constant. A reference structure (e.g. coord) has to be provided.- flag
--ewin <REAL>- description
Set the energy threshold to REAL kcal/mol. This affects several runtypes and the
[DEFAULT]is depending on the application (6 kcal/mol conformational searches, 30 kcal/mol screening tools).- flag
--prsc- description
Create a scoord.`*` file for each conformer in the
TURBOMOLEformat.- flag
--rthr <REAL>- description
Set RMSD threshold in Ångström. The
[DEFAULT]is 0.125 Å.- flag
--ethr <REAL>- description
Set energy threshold between conformer pairs in kcal/mol. The
[DEFAULT]is 0.05 kcal/mol.- flag
--bthr <REAL>- description
Set lower bound for the rotational constant threshold to REAL. The
[DEFAULT]is 0.01 (= 1%). The thresold is dynamically adjusted between this value and 2.5%, based on the anisotropy of the rotational constants.- flag
--nmr, --eqv, --entropy- description
Activate determination and printout of NMR-equivalencies. Writes the files
anmr_rotamerandanmr_nucinfo, which are required by theENSOpython script.- flag
--athr <REAL>- description
Similarity threshold to determine internal rotation equal atoms for NMR. The
[DEFAULT]is 0.04.- flag
-temp <REAL>- description
Set temperature for the calculation of Boltzmann weights. The
[DEFAULT]is 298.15 K.- flag
--esort- description
Sort only based on energy (i.e., no RMSD and rotational constant comparison)
- flag
--nowr- description
Don´t write new ensemble files (crest_rotamers_`*`.xyz, crest_conformers.xyz)
- flag
--subrmsd- description
Compare only those parts of the structure that were also included in the metadynamics bias potential. Can be important for constrained conformational searches.
- flag
--notopo- description
Turn off the initial topology check of the structures in the ensemble.
An extension to the CREGEN sorting is an automatic principle component analysis (PCA) and
k-Means sorting clustering algorithm. It can be invoked with the --cluster command.
- flag
--cluster <INT>- description
Perform a clustering on the final CREGEN ensemble to identify INT most representative structures, based on dihedral angles. Note that this algorithm currently does not work well for non-covalent complexes or molecular clusters and should only be applied to singular molecules.
Options¶
Calculation settings passed to xtb¶
- Method selection
- flag
--gfn2, --gfn1, --gfn0, --gfnff- description
Use any of the respective GFNn methods. The default is GFN2-xTB, but GFN-FF is strongly recommended for faster sampling.
- Charge and multiplicity
- flag
--chrg <INT>- description
Specify molecular charge as INT, overrides
.CHRGfile.- flag
--uhf <INT>- description
Specify \(N_{\alpha}-N_{\beta}\) as INT, overrides
.UHFfile
- Implicit solvation
- flag
--g, --gbsa <SOLVENT>- description
Generalized born (GB) model with solvent accessable surface (SASA) model, for available SOLVENT options se ref:gbsa`. The solvent input is not case-sensitive.
- flag
--alpb <SOLVENT>- description
New ALPB implicit solvation model, for available SOLVENT options se ref:gbsa`. The solvent input is not case-sensitive.
- Geometry optimization thresholds
- flag
--opt <LEVEL>- description
Set the optimization accuracy for final GFNn–xTB optimizations. See Geometry Optimization for valid LEVEL arguments. The
[DEFAULT]is vtight.
Options for conformational search algorithms¶
- Z-matrix sorting (see also
--zsortabove) - flag
--zs- description
Perform z-matrix sorting (i.e. ZSORT) for the input coordinate file.
- flag
--nozs- description
[DEFAULT]Do not perform z-matrix sorting of the input file.
- Genetic Z-matrix crossing
- flag
--cross- description
[DEFAULT]Perform Z-matrix strucutre crossing (GC) in the algorithm.- flag
--nocross- description
Skip Z-matrix strucutre crossing.
- Additional MD sampling after MTD
- flag
--norotmd- description
Turn off the additional MDs on the lowest conformers after the MTD step.
- flag
--tnmd <REAL>- description
Set temperature for the additional normal MDs on the lowest conformers after the MTD step. The
[DEFAULT]is 400 K.
- Adjsuting iterative behavior of iMTD-GC
- flag
--mrest <INT>- description
Maximum number of MTD restarts in iMTD-GC algorithm. The
[DEFAULT]is 5 cycles.
- Special settings for the iMTD-GC workflow
- flag
--quick- description
Perform a search with reduced settings for a crude conformer ensemble.
- flag
--squick, --superquick- description
Perform an even more crude conformational search than with
-quick.- flag
--mquick- description
Perform an even more crude conformational search than with
-quickor-squick.- flag
--nci- description
Specialized NCI mode that can be used to find aggregates of NCI complexes. The option generates an ellipsoide potential around the input structure and adds it to the MTD simulation. Also, settings for \(k\) and \(\alpha\) are adjusted and some settings are reduced, in order to achieve lower computation times.
- flag
---wscal <REAL>- description
Scale the ellipsoide potential axes in the
--ncimode by factor REAL.
- Technical iMTD-GC settings
- flag
--keepdir- description
Keep sub-directories of the conformer production run.
- Property mode appendix
- flag
--prop <STR>- description
This initializes the usage of the “property” mode as an appendix to the regular conformational search.
STR defines what shall be done with the ensemble. Valid options for STR are currently (case sensitive!):
- option
hess- performs a hessian calculation for all conformers and re-weights the ensemble on free energies- option
reopt- reoptimization of the ensemble with vtight thresholds (usefull for “quick” runs)- option
autoIR- calculate vib. modes for all conformers and average them (weighted by Boltzmann populations) in a single “crest.vibspectum” file.- flag
--for,--forall <FILE>- description
Instead of starting the property calculation on the final conformer ensemble file after iMTD-GC the property mode can directly be started for a given input ensemble <FILE> in the Xmol (*.xyz) format.
Note
The different quick, NCI and property settings are incompatible with --entropy!
- Entropy mode settings
- flag
--scthr,--entropy_cthr <REAL>- description
Specifiy the ensemble growth threshold (% new conformers) for
--entropyand--v4convergence. The default is 0.02 (=2%) for the entropy mode and 0.05 (=5%) for--v4.- flag
--ssthr,--entropy_sthr <REAL>- description
Specifiy the entropy growth threshold (% growth entropy) for
--entropyand--v4convergence. The default is 0.005 (=0.5%) for the entropy mode and 0.01 (=1%) for--v4.- flag
--trange <from> <to> <step>- description
Entropies from the
--entropymode are always printed for a range of temperatures. The respective temperatures can be specified with this option.- flag
--ptot <REAL>- description
For the rovibrational average \(\overline{S}_{msRRHO}\) requires frequency calculations at GFN level. To reduce computational cost, only the specified REAL fraction of structures are calculated, and the rest is averaged. The default is 0.9 (=90%).
- flag
--fscal <REAL>- description
Scale frequencies read for \(\overline{S}_{msRRHO}\) by a given factor. Also works together with the
--thermooption (see below, section Other Tools)- flag
--rotorcut,--sthr- description
Specify the rotor cutoff for the ro/vib entropy interpolation (\(\tau\)). Also works together with the
--thermooption (see below, section Other Tools)
Example applications¶
Contents
iMTD-GC conformational search¶
The default application of CREST is the iMTD-GC conformational search as described in section Introduction to CREST.
In the following a standard production run with this workflow is shown for the alanineglycine molecule.
The structure is given as:
> cat struc.xyz
20
C 2.081440 0.615100 -0.508430
C 2.742230 1.824030 -1.200820
N 4.117790 1.799870 -1.190410
C 4.943570 2.827040 -1.822060
C 6.440080 2.569360 -1.637600
O 7.351600 3.252270 -2.069090
N 0.610100 0.695090 -0.538780
O 2.095560 2.724940 -1.739670
O 6.705220 1.463410 -0.897460
H 0.303080 1.426060 0.103770
H 0.338420 1.050680 -1.460480
C 2.488753 -0.593400 -1.198448
H 2.416500 0.557400 0.532050
H 4.614100 1.081980 -0.670550
H 4.699850 3.794460 -1.373720
H 4.722890 2.844690 -2.894180
H 7.687400 1.448620 -0.860340
H 2.029201 -1.457008 -0.719999
H 2.170233 -0.542411 -2.238576
H 3.572730 -0.688405 -1.154998
Input structure of the alanineglycine molecule.¶
Let’s assume that we are interested in the conformations of Ala-Gly at the GFN2-xTB level with GBSA implicit solvation for water, and that we are using 4 CPUs. Then the command to invoke the conformational search would be:
> crest struc.xyz -gfn2 -g h2o -T 4
Tip
It usually is wise to preoptimze your input structure with xtb at the same level on which
the conformational search shall be conducted. Since the input structure is taken as a reference
for several sanity checks within the CREGEN routine, such as unchanging coordination numbers
of the atoms, providing a structure on the same level of theory is recommended.
The program call first creates a coord file from the given input structure and sorts the z-matrix (ZSORT).
Then the length of the MTD simulation is determined and the algorithm is started.
The following output can be expected (some printout was discarded for the documentation):
==============================================
| |
| C R E S T |
| |
| Conformer-Rotamer Ensemble Sampling Tool |
| based on the GFN-xTB method |
| S.Grimme, P.Pracht |
| Universitaet Bonn, MCTC |
==============================================
Version 2.7.0, Mon 24. Jun 11:41:02 CEST 2019
Using the GFN-xTB code.
Compatible with XTB version 6.1 and later.
-------------------------
Starting z-matrix sorting
-------------------------
total number of atoms : 20
total number of frags : 1
terminated normally
------------------------------------------------
Generating MTD length from a flexibility measure
------------------------------------------------
Calculating WBOs... done.
flexibility measure : 0.821
-------------------------------------
Starting a trial MTD to test settings
-------------------------------------
Success!
Estimated runtime for one MTD (5.0 ps) on a single thread: 16 sec
Estimated runtime for a batch of 14 MTDs on 4 threads: 1 min 4 sec
*******************************************************************************************
** N E W I T E R A T I O N C Y C L E **
*******************************************************************************************
========================================
MTD Iteration 1
========================================
========================================
| Meta-MD (MTD) Sampling |
========================================
<.......>
<.......>
-----------------------
Multilevel Optimization
-----------------------
-------------------------
1. crude pre-optimization
-------------------------
writing TMPCONF* Dirs from file "crest_rotamers_0.xyz" ... done.
Starting optimization of generated structures
<.......>
353 structures remain within 12.00 kcal/mol window
-------------------------------------
2. optimization with tight thresholds
-------------------------------------
writing TMPCONF* Dirs from file "crest_rotamers_1.xyz" ... done.
Starting optimization of generated structures
<.......>
90 structures remain within 6.00 kcal/mol window
========================================
MTD Iteration 2
========================================
<.......>
<.......>
========================================
MTD Iterations done
========================================
Collecting ensmbles.
running RMSDs... done.
E lowest : -33.88024
132 structures remain within 6.00 kcal/mol window
-----------------------------------------------
Additional regular MDs on lowest 4 conformer(s)
-----------------------------------------------
<.......>
Appending file crest_rotamers_1.xyz with new structures
-------------------------------------------
Ensemble optimization with tight thresholds
-------------------------------------------
writing TMPCONF* Dirs from file "crest_rotamers_1.xyz" ... done.
Starting optimization of generated structures
<.......>
136 structures remain within 6.00 kcal/mol window
========================================
| Structure Crossing (GC) |
========================================
input file name : crest_rotamers_3.xyz
number of atoms : 20
number of points on xyz files : 136
conformer energy window /kcal : 6.00
CN per atom difference cut-off : 0.3000
RMSD threshold : 0.2500
max. # of generated structures : 250
reading xyz file ...
# in E window 136
generating pairs ... 9315
91.2 % done
generated pairs : 7838
number of clash discarded : 1342
average rmsd w.r.t input : 2.82902
sd of ensemble : 0.63747
number of new structures : 116
removed identical structures : 384
<.......>
<.......>
================================================
| Final Geometry Optimization |
================================================
---------------------
Ensemble optimization
---------------------
writing TMPCONF* Dirs from file "crest_rotamers_4.xyz" ... done.
Starting optimization of generated structures
126 structures remain within 6.00 kcal/mol window
-------------------------------------
CREGEN - CONFORMER SYMMETRY ANALYSIS
-------------------------------------
input file name : crest_rotamers_5.xyz
output file name : crest_rotamers_6.xyz
number of atoms : 20
number of points on xyz files : 159
RMSD threshold : 0.1250
Bconst threshold : 0.0200
population threshold : 0.0500
conformer energy window /kcal : 6.0000
# fragment in coord : 1
number of reliable points : 159
reference state Etot : -33.8802301686000
number of doubles removed by rot/RMSD : 33
total number unique points considered further : 126
Erel/kcal Etot weight/tot conformer set degen origin
1 0.000 -33.88023 0.04725 0.28280 1 6 mtd10
2 0.000 -33.88023 0.04725 md1
3 0.000 -33.88023 0.04724 mtd1
4 0.001 -33.88023 0.04718 gc
5 0.003 -33.88022 0.04698 md3
6 0.005 -33.88022 0.04689 gc
7 0.043 -33.88016 0.04392 0.17556 2 4 md5
8 0.043 -33.88016 0.04391 mtd10
9 0.044 -33.88016 0.04391 mtd9
10 0.045 -33.88016 0.04383 mtd2
11 0.477 -33.87947 0.02116 0.06323 3 3 mtd5
12 0.478 -33.87947 0.02112 md6
13 0.482 -33.87946 0.02096 mtd9
14 .....
15 .....
.......
.......
CREST terminated normally.
The production run yields 126 structures of Ala-Gly, distributed over 51 different conformers within 6 kcal/mol above the lowest conformer that was found at the GFN2-xTB level.
Three lowest conformers of alanineglycine generated by CREST at the GFN2-xTB level.¶
The final ensemble of all the found conformers is written to an ensemble file in the Xmol format called crest_conformers.xyz.
The corresponding CRE, i.e., the ensemble containing also the rotamers is written to the file crest_rotamers.xyz.
Sorting an ensemble¶
The CREGEN routine that is used within the conformational search can also be used as an standalone tool. To use this you can simply call the routine by:
> crest struc.xyz -cregen ensemble.xyz
Here ensemble.xyz is the ensemble file that contains all the structures in the Xmol format.
Note
It is required to present a single reference structure (struc.xyz in the example above) of the molecule to check for
CN clashes. Also, all structurues in the ensemble must have the same atom order.
Comparing two ensemble¶
Two ensembles generated on different levels of theory can be compared with the -compare option.
Let’s assume that there are two ensembles v1.xyz, generated with the MF-MD-GC procedure and v2.xyz,
generated with the default iMTD-GC workflow.
To compare the 5 lowest conformers of each ensemble simply call:
> crest struc.xyz -compare v1.xyz v2.xyz -maxcomp 5
Which produces the output:
==============================================
| |
| C R E S T |
| |
| Conformer-Rotamer Ensemble Sampling Tool |
| based on the GFN-xTB method |
| S.Grimme, P.Pracht |
| Universitaet Bonn, MCTC |
==============================================
Version 2.7, Thu 27. Jun 13:41:37 CEST 2019
Using the GFN-xTB code.
Compatible with XTB version 6.1 and later.
---------------------
Sorting file <v1.xyz>
---------------------
running RMSDs... done.
File <v1.xyz> contains 240 conformers.
The 5 lowest conformers will be taken for the comparison:
conformer #rotamers
1 1
2 5
3 3
4 1
5 2
---------------------
Sorting file <v2.xyz>
---------------------
running RMSDs... done.
File <v2.xyz> contains 51 conformers.
The 5 lowest conformers will be taken for the comparison:
conformer #rotamers
1 6
2 4
3 3
4 6
5 4
-----------------------
Comparing the Ensembles
-----------------------
Calculating RMSDs between conformers... done.
RMSD threshold: 0.1250 Å
RMSD matrix:
conformer 1 2 3 4 5
1 0.01727 1.44147 1.56327 0.81845 0.83933
2 0.00791 1.43084 1.56995 0.79512 0.83992
3 1.43350 0.01254 0.80724 1.58138 1.59243
4 0.12794 1.40597 1.54663 0.89315 0.83634
5 0.14626 1.51398 1.56167 0.68473 0.88006
--------------------------------
Correlation between Conformers :
--------------------------------
# Ensemble A # Ensemble B
5 -33.87887
4 -33.87937
3 -33.87947
5 -33.88008
4 -33.88011
3 -33.88017 <----> 2 -33.88016
2 -33.88023 <----> 1 -33.88023
1 -33.88023
-----------------
Wall Time Summary
-----------------
--------------------
Overall wall time : 0h : 0m : 0s
CREST terminated normally.
From the output it can be seen that there is a correlation between the lowest conformers,
i.e., the lowest conformers were found by both workflows.
As the display options in the terminal are limited, an addtional file called rmsdmatch.dat is written,
from which the exact correlation between the conformers of the two ensembles can be read.
If, for example, two different levels of theory are used and the energies of the molecules in both ensembles
are too different, then the output will not be of much use and one must refer to the rmsdmatch.dat file.
> cat rmsdmatch.dat
1 1
2 1
3 2
Each line in this file consists of only two values a and b which denote that conformer a from ensemble A matches conformer b from ensemble B. In the example case shown above, the MF-MD-GC produced the lowest conformer twice, which both naturally match conformer 1 from the iMTD-GC procedure. The second conformer also is the same in both ensembles.
Note
In order for the comparison to work, both ensembles must have the same number of atoms with the same atom order in each structure. Furthermore the ensembles should be full CREs, i.e., rotamers should be present.
Constrained conformational sampling¶
Warning
The following application is still under development and should be considered an experimental feature.
It is possible to include additional constraints to all xtb calculations
that are conducted by CREST. To do this one has to create a file called
.constrains (or .xcontrol, both is valid) in the working directory, which contains the constraints
in the exact same syntax as used by the xtb (see section Detailed Input)
Constraints that are included via the .constrains file will be included in ALL calculations
of the conformer search run.
To circumvent name conventions a constrainement file under arbitrary name can directly be provided
by the -cinp <FILE> option.
Since this can overwrite settings created by CREST it should only be used very cautiously!
The main application for the additional constraints is the constrainment (fixing) of atoms, which could for example be used to sample only conformations for parts of a molecule. Another use could be the sampling of conformers for the transition state of an reaction.
To fix atoms it is also recommended to use an reference input file additionally to the
normal structure input file, which is done with the argument reference=FILE in the .xcontrol file.
Furthermore, fixed atoms should not be included in the RMSD of the MTD collective variables.
The content of the .xcontrol file for fixing atoms should look like the following example:
> cat .xcontrol
$constrain
atoms: 4,8,10,12 # atoms 4, 8, 10 and 12 of some example molecule shall be constrained
force constant=0.5
reference=coord.original # name of the reference file (just a copy of the input coord-file)
$metadyn
atoms: 1-3,5-7,9,11 # atoms *included* to RMSD in the MTD (typically NOT the constrained atoms)
$end
This should ensure correct constrainment (as far as possible) in the MTD, as well as in the GFNn-xTB geometry
optimization within a CREST run.
It is also possible to let CREST generate such a file automatically.
To do this the list of atoms has to be provided with the flag --constrain <atom list>, i.e.,
> crest coord --constrain <atom list>
which will not start any calculation but instead write a file .xcontrol.sample that could subsequentially be used.
Furthermore the file coord.ref will be created. (e.g. for a molecule with 65 atoms):
> crest coord --constrain 1,2,3,26-30
==============================================
| |
| C R E S T |
| |
| Conformer-Rotamer Ensemble Sampling Tool |
| based on the GFN-xTB method |
| P.Pracht, S.Grimme |
| Universitaet Bonn, MCTC |
==============================================
Version 2.8, Fri 25. Oct 12:04:52 CEST 2019
Using the GFN-xTB code.
Compatible with XTB version 6.1 and later.
Command line input:
> crest --constrain 1,2,3,26-30
Input list of atoms: 1,2,3,26-30
8 of 65 atoms will be constrained.
A reference coord file coord.ref was created.
The following will be written to <.xcontrol.sample>:
> $constrain
> atoms: 1-3,26-30
> force constant=0.5
> reference=coord.ref
> $metadyn
> atoms: 4-25,31-65
> $end
<.xcontrol.sample> written. exit.
Note
Important: <atom list> must not contain any blanks and atoms must be seperated by comma. Ranges (e.g. 26-30) are allowed.
Sampling of noncovalent complexes and aggregates (NCI mode)¶
A specialized application of CREST is the sampling of aggregates (also refered to as NCI mode).
The idea here is to find different conformations of non-covalently bound complexes in which the
arrangement of the fragments is of interest.
The application can be called by:
> crest struc.xyz -nci
The procedure and output is essentially the same as a normal iMTD-GC production run, but with reduced settings (less MTDs, different \(k\) and \(\alpha\)), and no genetic structure crossing. What is different, however, is that first a ellipsoide wall potential is created and added to the meta-dynamics. A nice example for this application are small molecular clusters, e.g. (H2O)6. The ellipsoide potential that is automatically determined for the input cluster is visualized in the figure below.
Visualization of an ellipsoide potential around (H2O)6 cluster.¶
The ellipsoide potential is required in the MTDs to counteract the bias potential, which would simply lead to a dissociation of the NCI complex after a few pico seconds (due to the maximization of the RMSD). In the subsequent geometry optimization, however, the surrounding potential must not be present since the bias potential is also not there and the structure would be artificially compressed by the ellipsoide. Hence it is automatically removed in the geometry optimizations
Note
The ellipsoide potential can be scaled by the factor REAL with the flag -wscal REAL.
Many new clusters are generated even for small NCI complexes, typically much more than conformers are generated for a single medium sized molecule.
In general, the task of finding new low lying aggregates is much more challenging than finding (only) conformers, since each fragment of
the complex could also have several different low lying conformations.
For the (H2O)6 cluster 3 examples are shown in the figure below. Note that all three structures are also part of the
well established WATER27 benchmark set, but were generated automatically by CREST from a single input structure. In total 69 different clusters were
found of which only 3 are shown.
Three automatically generated structures for a (H2O)6 cluster.¶
Molecular prototropy screening¶
Protonation site screening¶
The screening for possible protonation sites, i.e., for the different protomers of an molecule is possible by using a localized molecular orbital LMO approach. Herein, first the \(\pi\)- and LP-centers are determined by a GFNn-xTB calculation, and then all possible input structures are generated where a proton is placed at one of these centers. This procedure was first described in J. Comput. Chem., 2017, 38, 2618–2631.
The example calculation is performed for alanineglycine, in the gas phase, with the command
> crest struc.xyz -protonate
Which returns the following output:
==============================================
| |
| C R E S T |
| |
| Conformer-Rotamer Ensemble Sampling Tool |
| based on the GFN-xTB method |
| S.Grimme, P.Pracht |
| Universitaet Bonn, MCTC |
==============================================
Version 2.7.0, Mon 24. Jun 11:41:02 CEST 2019
Using the GFN-xTB code.
Compatible with XTB version 6.1 and later.
__________________________________________
| |
| automated protonation script |
|__________________________________________|
LMO calculation ... done.
-----------------------
Multilevel Optimization
-----------------------
-------------------------
1. crude pre-optimization
-------------------------
writing TMPCONF* Dirs from file "protonate_0.xyz" ... done.
Starting optimization of generated structures
<.......>
Now appending opt.xyz file with new structures
12 structures remain within 90.00 kcal/mol window
---------------------
2. loose optimization
---------------------
writing TMPCONF* Dirs from file "protonate_1.xyz" ... done.
Starting optimization of generated structures
<.......>
Now appending opt.xyz file with new structures
Structures sorted out due to dissociation: 1
11 structures remain within 60.00 kcal/mol window
--------------------------------------------
3. optimization with user-defined thresholds
--------------------------------------------
writing TMPCONF* Dirs from file "protonate_2.xyz" ... done.
Starting optimization of generated structures
<.......>
Now appending opt.xyz file with new structures
9 structures remain within 30.00 kcal/mol window
===================================================
Identifying topologically equivalent structures:
Equivalent to 1. structure: 2 structure(s).
Equivalent to 3. structure: 5 structure(s).
Equivalent to 5. structure: 2 structure(s).
Done.
Appending file <protonated.xyz> with structures.
Initial 9 structures from file protonate_3.xyz have
been reduced to 3 topologically unique structures.
===================================================
============= ordered structure list ==============
===================================================
written to file <protonated.xyz>
structure ΔE(kcal/mol) Etot(Eh)
1 0.00 -33.964453
2 3.51 -33.958853
3 5.75 -33.955296
-----------------
Wall Time Summary
-----------------
LMO calc. wall time : 0h : 0m : 0s
multilevel OPT wall time : 0h : 0m : 3s
--------------------
Overall wall time : 0h : 0m : 4s
CREST terminated normally.
As one can see from the output, three possible protomers of alanineglycine were found at the GFN2-xTB level (within the default
30 kcal/mol energy window around the most stable protomer). This ensemble of structures is written to a file called
protomers.xyz.
The first (lowest) protomer created by CREST for this molecule includes a ring-closure, apparently caused by the addition of the proton.
This nicely demonstrates the ability of our approach to form and break new bonds.
The three protomers are shown in the figure below.
Three lowest protomers of alanineglycine generated by CREST at the GFN2-xTB level.¶
Deprotonation site screening¶
The general approach to find deprotonation sites at a GFN level is much more simple than finding protonation sites. For each hydrogen atom in the structure a new (deprotonated) reference structure is created and optimized in a multilevel approach. The commandline argument to invoke this search is:
> crest struc.xyz -deprotonate
For the example of alanineglycine, again three structures are obtained and written to a file called deprotonated.xyz:
<.......>
<.......>
===================================================
============= ordered structure list ==============
===================================================
written to file <deprotonated.xyz>
structure ΔE(kcal/mol) Etot(Eh)
1 0.00 -33.593702
2 21.83 -33.558913
3 25.12 -33.553669
<.......>
<.......>
However, two of the three structures have much higher energies and therefore mainly the lowest deprotomer should be considered.
Lowest deprotomer of alanineglycine at the GFN2-xTB level. The deprotonation happens at the carboxyl group.¶
Tautomerization screening¶
The last application of the different prototropy screening protocols is an automatized tautomerization tool, which utilizes
both the protonation and deprotonation procedures presented in the previous two subsections.
By first protonating a molecule and then deprotonation of the resulting protomers at all postions, prototropic tautomers
relative to the initial input structure can be found.
A single cycle of this protonation/deprotonation in principle yields all tautomers with a single hydrogen permutation relative to the input.
If a higher number of hydrogen permutations is required, the procedure can simply be repeated with the created tautomers, i.e., tautomers with
two or more hydrogen atom permutations are generated.
From experience, however, it is generally sufficient to repeat this protonation/deprotonation cycle twice (which is the default in CREST),
in order to get the relevant low energy tautomers.
The approach was first described in J. Comput.-Aided Mol. Des., 2018, 32, 1139-1149.
The tautomerization search can be conducted by the command
> crest struc.xyz -tautomerize
Tip
The number of protonation/deprotonation cycles can be adjustet with the flag -iter INT, where INT is the number of cycles.
For alanineglycine the following output is generated:
==============================================
| |
| C R E S T |
| |
| Conformer-Rotamer Ensemble Sampling Tool |
| based on the GFN-xTB method |
| S.Grimme, P.Pracht |
| Universitaet Bonn, MCTC |
==============================================
Version 2.7.0, Mon 24. Jun 11:41:02 CEST 2019
Using the GFN-xTB code.
Compatible with XTB version 6.1 and later.
__________________________________________
| |
| automated tautomerization script |
|__________________________________________|
*******************************************************************************************
** P R O T O N A T I O N C Y C L E 1 of 2 **
*******************************************************************************************
LMO calculation ... done.
-----------------------
Multilevel Optimization
-----------------------
<.......>
===================================================
Identifying topologically equivalent structures:
<.......>
Appending file <protonated.xyz> with structures.
Initial 9 structures from file protonate_2.xyz have
been reduced to 3 topologically unique structures.
===================================================
============= ordered structure list ==============
===================================================
written to file <protonated.xyz>
structure ΔE(kcal/mol) Etot(Eh)
1 0.00 -33.964400
2 3.60 -33.958659
3 5.78 -33.955188
*******************************************************************************************
** D E P R O T O N A T I O N C Y C L E 1 of 2 **
*******************************************************************************************
-----------------------
Multilevel Optimization
-----------------------
<.......>
===================================================
Identifying topologically equivalent structures:
<.......>
Appending file <deprotonated.xyz> with structures.
Initial 24 structures from file deprotonate_2.xyz have
been reduced to 8 topologically unique structures.
===================================================
============= ordered structure list ==============
===================================================
written to file <deprotonated.xyz>
structure ΔE(kcal/mol) Etot(Eh)
<.......>
*******************************************************************************************
** P R O T O N A T I O N C Y C L E 2 of 2 **
*******************************************************************************************
Calculating LMOs for all structures in file <tautomerize_1.xyz>
<.......>
Collecting generated protomers ... done.
-----------------------
Multilevel Optimization
-----------------------
<.......>
===================================================
Identifying topologically equivalent structures:
<.......>
Appending file <protonated.xyz> with structures.
Initial 51 structures from file protonate_1.xyz have
been reduced to 17 topologically unique structures.
===================================================
============= ordered structure list ==============
===================================================
written to file <protonated.xyz>
structure ΔE(kcal/mol) Etot(Eh)
<.......>
*******************************************************************************************
** D E P R O T O N A T I O N C Y C L E 2 of 2 **
*******************************************************************************************
-----------------------
Multilevel Optimization
-----------------------
<.......>
===================================================
Identifying topologically equivalent structures:
<.......>
Appending file <deprotonated.xyz> with structures.
Initial 95 structures from file deprotonate_2.xyz have
been reduced to 19 topologically unique structures.
===================================================
============= ordered structure list ==============
===================================================
written to file <deprotonated.xyz>
structure ΔE(kcal/mol) Etot(Eh)
<.......>
*******************************************************************************************
** T A U T O M E R I Z E **
*******************************************************************************************
---------------------------
Final Geometry Optimization
---------------------------
<.......>
===================================================
Identifying topologically equivalent structures:
Done.
Appending file <tautomers.xyz> with structures.
All initial 19 structures from file tautomerize_4.xyz are unique.
===================================================
============= ordered structure list ==============
===================================================
written to file <tautomers.xyz>
structure ΔE(kcal/mol) Etot(Eh)
1 0.00 -33.867777
2 1.99 -33.864606
3 3.84 -33.861657
4 3.84 -33.861656
5 4.42 -33.860731
6 4.68 -33.860314
7 10.63 -33.850839
8 10.79 -33.850575
9 10.92 -33.850381
10 10.95 -33.850329
11 12.18 -33.848371
12 12.18 -33.848371
13 13.45 -33.846343
14 19.21 -33.837164
15 19.21 -33.837164
16 20.24 -33.835520
17 24.97 -33.827984
18 25.58 -33.827014
19 29.53 -33.820725
-----------------
Wall Time Summary
-----------------
LMO calc. wall time : 0h : 0m : 0s
multilevel OPT wall time : 0h : 0m :31s
--------------------
Overall wall time : 0h : 0m :32s
CREST terminated normally.
As can be seen from the output, the entire procedure is constructed from the protonation and deprotonation site screening routines.
The first protonation step yields the same three protomers that are also obtained by the standalone application, which are then
automatically deprotonated. Two protonation/deprotonation cycles are performed.
The final tautomer ensemble consists of 19 structures (within 30 kcal/mol) and is written to the file tautomers.xyz.
Property calculations on final ensemble¶
It is possible to (automatically) perform further calculations on the final conformer ensemble
by the usage of the -prop option:
> crest [input] [options] -prop [property option]
Currently there are only some few options available but we plan to implement more.
A useful type of this mode, e.g. is the the reoptimization of the conformer ensemble with
very tight convergence thresholds. In combination with crude conformational search settings
such as -qucik, -squick or -mquick this helps to ensure the ensemble convergence,
i.e., the minimization of artificial structural differences for the same conformer due to
too loose geometry optimizations.
This reoptimization can be requested by
> crest coord -mquick -prop reopt
Updated geometries will generally be written to a new ensemble file called crest_property.xyz.
Another useful runtype of this mode is the calculation of frequencies and reweighting of the conformers on the resulting free energies. E.g.:
> crest coord -prop hess
The property mode can also directly be applied to a given ensemble:
> crest -forall <ensemble>.xyz -prop [property option]
Dry run to check settings prior to calculations¶
A dry run can be performed by CREST to verify the settings that would be applied in the
calculation. To do this, simply add the -dry flag to the cmd-input line.
> crest [input] [options] -dry
Whit this option nothing will be actually be calculated but instead the settings are printed. E.g. for some random setting:
> crest coord -ewin 3.2 -temp 999 -gfn1 -nozs -chrg 1 -cinp .xcontrol.sample -dry
<....>
<....>
*******************************************************************************************
** D R Y R U N **
*******************************************************************************************
Dry run was requested.
Running CREST with the chosen cmd arguments will result in the following settings:
Input file : coord
Job type :
1. Conformational search via the iMTD-GC algo
Job settings
sort Z-matrix : F
CRE settings
energy window (-ewin) : 3.2000
RMSD threshold (-rthr) : 0.1250
energy threshold (-ethr) : 0.1000
rot. const. threshold (-bthr) : 0.0200
T (for boltz. weight) (-temp) : 999.00
General MD/MTD settings
simulation length [ps] (-len) : <system dependent>
time step [fs] (-tstep) : 5.0
shake mode (-shake) : 2
MTD temperature [K] (-mdtemp) : 300.00
trj dump step [fs] (-mddump) : 100
MTD Vbias dump [ps] (-vbdump) : 1.0
Constrainment info
applying constraints? : T
constraining file : .xcontrol.sample
file content :
> $constrain
> atoms: 1-3,26-30
> force constant=0.5
> reference=coord.ref
> $metadyn
> atoms: 4-25,31-65
> $end
XTB settings
binary name (-xnam) : xtb
GFN method (-gfn) : --gfn1
(final) opt level (-opt) : 2
Molecular charge (-chrg) : 1
Technical settings
working directory : /home/philipp/calculations/cresttest
CPUs (threads) (-T) : 4
normal dry run termination.
Examples from the paper: Automated exploration of the low-energy chemical space with fast quantum chemical methods¶
Conformers of transition-states¶
At first a transition-state (TS) has to be localized. Then the TS mode has to be identified and reasonable constrains have to be applied to freeze this mode during the CREST run. Choosing suitable constrains is the responsibility of the user.
Tranisition state of the active site of the COMT enzyme. TS mode highlighted in blue. (Mg2+ in green, sulfur in yellow).¶
In this example a methyl group is transfered onto the catechol molecule.
cat coord.ref
$coord
-2.57480197685137 -0.38573933229522 0.86228536590435 Mg
-5.87996595426622 -1.46598597135567 -1.00931632324148 O
-5.79755045954234 1.88737481602186 1.36486580018227 O
-6.93504356011937 0.41703174067196 -0.07677235660280 C
-9.68583177367761 0.93957235453071 -0.70260934507636 C
-9.88785370898918 2.90051382662291 -1.27585066001173 H
-10.31204304615949 -0.31693795001232 -2.19707799857187 H
-10.81224558069477 0.63532604630470 0.98871505743889 H
-1.35732893615725 2.84149984259631 3.74273757259152 O
-1.31788637685368 1.88478932440519 -1.80336662588251 O
-1.03506712269361 -3.09136305475668 -1.65209468828016 O
-3.01034174150676 3.35231258504990 4.30691490291278 H
-0.64007292100150 4.31049584542225 2.93186531615926 H
-3.02042382593105 -2.69109360436689 3.78441246580865 O
-0.67413309122153 -2.78784634989936 4.10013037720282 C
0.80704125300360 -1.59087682326574 2.72475235410942 O
0.37030033373577 -4.45667671167827 6.17913372417457 C
1.65729077111170 -3.36053569450090 7.34278701173010 H
-1.17079464125707 -5.18933342363882 7.31676317209597 H
1.41212360996512 -6.00880794547076 5.32805483610633 H
-0.04610218809699 0.99217247488345 -2.84947633284740 H
-0.58166801572397 4.35407649708453 -2.13719082516246 C
1.69930763718877 4.60968100984284 -3.53188509022323 C
-1.89895861199073 6.41295502711680 -1.26089925937752 C
2.61815567802848 7.04758861150735 -3.94211016089909 C
-0.94293511850593 8.82264113991643 -1.71734825726509 C
-3.65794447068903 6.13213826999732 -0.25859371242962 H
1.29133066638906 9.11831895867148 -3.04019344765619 C
4.35136261809131 7.29515670682662 -4.99253235854911 H
-1.96139641783255 10.45433175989920 -1.03894063047482 H
2.01793975704253 10.99527109251927 -3.38477251662235 H
5.63677744964081 -0.19526366812337 -3.54734464996746 H
3.55857435122244 0.44545364581733 -0.79647639427433 H
6.02794370271953 2.75567866080431 -1.74563412676399 H
2.74773927853638 2.50310064429053 -4.32763740793204 O
5.16232303152189 0.93488296527549 -1.93713143185301 C
7.77908129622702 -0.95480533027442 0.60724611364076 S
6.20470140355368 -3.99408071134196 0.68137239550646 C
7.00770708640275 -5.10883646299712 2.20213746286551 H
4.19551348270129 -3.68373090740626 0.97362752914345 H
6.54643468112530 -4.90904155689111 -1.11917138292065 H
6.61325357496481 0.34737209228094 3.55003016825311 C
7.52593267335208 -0.62757026577676 5.10500275305939 H
7.10342021330197 2.33658535430792 3.58672294810726 H
4.57513571292400 0.10172782556556 3.62256009227771 H
-1.61022171124489 -5.31411191371024 -2.02789529853598 C
-3.17527947979499 -6.57718946281529 -0.51674594958634 N
-3.77763814894346 -8.33207207055257 -0.93763600526181 H
-4.05833804986482 -5.57635320116590 0.85099090510650 H
-0.47266612030322 -6.78426594278943 -4.18601622917577 C
0.51805850799787 -8.43374379675092 -3.46937160488911 H
-1.96305386150678 -7.41025810365247 -5.45278966275112 H
0.83013814067146 -5.58152886274452 -5.21822759129119 H
$end
To preserve the TS vibrational mode the atoms which are dominantly contributing to this mode are fixed. In this case the carbon (36) of the methyl group being transferred, the sulfur (37) of the S-adenosyl- L -methionine (SAM) and the oxygen (35) of the catechol group are constrained. For running the TS conformational search only these atoms have to be constrained. But to retain the surrounding enzyme environment additionally the distances of all ligands to the magnesium cation and the amide magnesium water angle were constrained. As stated before all atoms with constrains have to be removed from the list of atoms which are used in the metadynamics simulation.
$constrain
atoms: 35-37
force constant=0.5
reference=coord.ref
distance: 10, 1, auto
distance: 2, 1, auto
distance: 11, 1, auto
distance: 14, 1, auto
distance: 9, 1, auto
angle: 9, 1, 11, 180
$metadyn
atoms: 3-8,12-13,15-34,38-53
$end
crest coord -cinp .constraintinp -g methanol > crest.out
The TS conformer search yields 141 conformers within 6 kcal/mol. On these conformers hessians have to be calculated to ensure that the transition-state mode is preserved. Those conformers with preserved mode can be optimized into the TS and the true TSs have to be confirmed by again a hessian calculation (only one imaginary mode). During the optimization some conformers can become identical or rotamers of each other. To this end all optimized geometries are appended and sorted with the cregen sorting routine.
cat TSconf*.xyz >> allts.xyz
crest coord -cregen allts.xyz -ewin 30 > sorting.out
Tranisition state conformers of the active site of the COMT enzyme. (Mg2+ in green, sulfur in yellow, water oxygen in blue). Hydrogen atoms are omitted for clarity.¶
Now after sorting only 91 unique TS conformers are optained within an energy window of 6.1 kcal/mol. This procedure can in principle be refinded at DFT level.
Conformers of metal-organic systems¶
trans-Cu(II)(L-valine)2
Calculation of trans-Cu(II)(L-valine)2 conformers in the gas phase.
cat coord
$coord
-0.002022192318 -0.000684522852 1.349121896005 CU
2.028671941135 2.818125977315 1.174767316951 O
4.406562542342 2.529552834523 0.838287117696 C
5.900488893190 4.242544277537 0.591753944418 O
5.382406579092 -0.254197829091 0.699650595616 C
3.456927714843 -1.958681435237 1.737975874213 N
3.442953703137 -3.661542617496 0.846227450863 H
3.710547158869 -2.249430796311 3.618554595139 H
7.133224715719 -0.349791899055 1.804782999185 H
6.007018333138 -0.877714812490 -2.069473442827 C
7.266213509953 -3.466799912264 -2.312238367182 C
8.881995597301 -3.618089140164 -1.050454618739 H
7.930334466002 -3.738254167109 -4.236839656939 H
5.952357752542 -4.994107920656 -1.890594175637 H
3.663534173447 -0.712885768717 -3.746419767180 C
4.156219468360 -1.164942859389 -5.689573088070 H
2.890265219159 1.189883399588 -3.704912704715 H
2.203522204085 -2.025873622846 -3.126878925482 H
7.355957431563 0.567207315613 -2.680683804317 H
-2.033163868813 -2.819780021566 1.179505209377 O
-4.409877555278 -2.530551975348 0.835068556898 C
-5.903043316660 -4.243023566156 0.580387940800 O
-5.384798675016 0.253509426488 0.697143335052 C
-3.461334991004 1.955672873602 1.742931448447 N
-3.448757571238 3.662158486139 0.858135081470 H
-3.716247763220 2.238184300034 3.624611253622 H
-7.138671974341 0.348502264395 1.797538738740 H
-6.001307995929 0.880859137312 -2.072901114603 C
-7.255902292489 3.472119634743 -2.316426880308 C
-7.917767124579 3.744910887179 -4.241612390481 H
-5.939710712311 4.997073845686 -1.893506102537 H
-8.872648523224 3.626011270865 -1.056195385178 H
-3.653380600330 0.714736239795 -3.743504646086 C
-2.884657484645 -1.189944325855 -3.704494974332 H
-2.192229886598 2.022965931298 -3.116395721134 H
-4.139423979729 1.172691111744 -5.686934420106 H
-7.350580840264 -0.561585906341 -2.689213500551 H
$end
crest coord -nci > crest.out
Results in 28 conformers within an energy window of 6 kcal/mol.
[Pt(COMe)2(2-py)3COH] conformers in methanol.
![[Pt(COMe)2(2-py)3COH] in methanol](_images/crest_pt.png)
cat coord
$coord
1.48235976014562 0.32575477023909 0.83983586742930 pt
4.37233116325056 -2.04701937728251 0.66066526359202 c
5.11582123352082 -2.89977152283009 -1.35531347223172 o
5.60331010456907 -2.97886601012202 3.10440618630801 c
5.11582123352082 -1.79782119213888 4.71363082065877 h
4.96457322302306 -4.90914755554552 3.43123243126445 h
7.64542186308448 -3.03767428737742 2.85382472163511 h
3.90413261656682 3.15849014823120 0.32067896584616 c
3.77547628198769 4.50973504009881 -1.55263489557537 o
5.78086877201500 3.82467530185737 2.40255812110202 c
6.44902868945004 5.75938447561023 2.16769917785472 h
4.93481948506077 3.56859662386391 4.26032709535443 h
7.38167845589603 2.54234683232997 2.24297074917982 h
-1.45880054444693 -2.37015120764916 1.99982157738756 n
-1.37380633216814 -3.71993156176379 4.12084829921227 c
-3.47313332880892 -4.91477704969539 5.12088380983082 c
-5.76730431783315 -4.67836853101913 3.87619679514437 c
-5.86160354159028 -3.26072055256804 1.67926544374004 c
-3.65812239940936 -2.14869231241016 0.79621720883004 c
-3.66283159693252 -0.54983471562441 -1.60480456492594 c
-1.36490194262998 -1.28858913220566 -3.20027766220770 c
-1.32606807059918 -3.74293708770554 -3.74494019740640 n
0.45445456851927 -4.60152659727760 -5.28248940926294 c
2.25936790283487 -3.06404352583571 -6.38168829870466 c
2.17878809080250 -0.49502320914006 -5.86813254537940 c
0.32467195716495 0.43733364975533 -4.26146660021256 c
0.14833216307473 2.45190076015779 -3.96574713712955 h
3.52744783732032 0.78490530819858 -6.70693851206628 h
3.68438581320421 -3.84772429150018 -7.60737222739882 h
0.39857914622211 -6.61487483432435 -5.63264243360372 h
-5.86517134452916 -0.98949461824931 -3.04219073283502 o
-5.69660399402350 -2.62769064394335 -3.83817172589844 h
-3.63492223167593 2.20020246734036 -0.78356738209650 c
-1.79344269668899 2.91320936536104 0.78584828153889 n
-1.75920841806563 5.28509912105245 1.61658700736449 c
-3.54797404257573 7.05739011313605 0.91252418313075 c
-5.45207721188036 6.32967358689699 -0.73330822586627 c
-5.50553000527517 3.85501674464698 -1.58299523562631 c
-6.94955289136293 3.18275045232518 -2.84989409127871 h
-6.87435123990475 7.65734792470912 -1.34159783995923 h
-3.43966438926938 8.95769115346132 1.63587922145511 h
-0.24274666012596 5.76489302728759 2.90140613593504 h
-7.59878342212486 -2.99720202278941 0.64743151148342 h
-7.44966324325272 -5.57429713925087 4.59918333687282 h
-3.30863455866736 -5.99888080678762 6.83682316863177 h
0.45096235462570 -3.84321729467325 5.03295296314152 h
$end
crest coord -g methanol -ewin 10 > crest.out
The search for the Pt-complex conformers results in 68 conformers within an energy window of 10 kcal/mol.
Conformational search of tyrosine on a graphene surface¶
To sample a tyrosine molecule at a graphene surface, the graphene sheet has to be constrained. All atoms in the graphene layer are constrained and removed from the metadynamics list.
cat .constrains
$constrain
atoms: 1-252
force constant=0.5
reference=coord.input-original
$metadyn
atoms: 253-276
$end
cat coord.input-original
$coord
25.57030991921202 -1.29059115296523 -0.00598160501741 C
25.57044241258889 1.28341269512943 -0.00397025649369 C
23.26056590790795 2.70217665940709 -0.00029100251731 C
23.24029402398585 5.32779404644931 0.00100734191172 C
20.94157103860908 6.71653777403401 0.00350095166658 C
20.91152361664611 9.36664222799565 0.00390218154564 C
18.62125921494789 10.73533662251798 0.00644642379287 C
18.58134086796354 13.40310199790359 0.00577252431633 C
16.30144187186615 14.75441822463413 0.00911453357094 C
16.24838174294015 17.43954219647988 0.00645557179198 C
13.98481323267349 18.77014376357869 0.00996412506652 C
13.91132086532623 21.47993962309619 0.00398308521361 C
11.68223395792687 22.76705405593083 0.00667868517840 C
23.23975279130400 -5.33474095446540 -0.00731302769541 C
23.26029458648507 -2.70912180306862 -0.00467349937707 C
20.93174016704535 -1.33727196043975 -0.00133108922934 C
20.93188342707722 1.33055529046503 0.00081585427198 C
18.61221093462830 2.68271748197896 0.00282646704916 C
18.60800793365893 5.36022077189572 0.00464910445605 C
16.29058723267624 6.70694827919018 0.00657403025646 C
16.28436011426403 9.38628406493185 0.00875170443409 C
13.96723583506467 10.73158318782874 0.01208246556117 C
13.95992943220878 13.41187709257133 0.01391081920492 C
11.64338138388279 14.75451471117306 0.01811199832376 C
11.63248103339880 17.43948496412882 0.01741770073639 C
9.32215273401024 18.77351998648383 0.02061202665840 C
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18.60745075594095 -5.36670680488450 -0.00374295822885 C
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13.96434116375503 2.68237236768262 0.00076404228717 C
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4.67042012951467 18.77581140475820 0.02736696446206 C
4.66258399962784 21.47489924179938 0.02293852266839 C
2.35249685077769 22.77391798267787 0.02212621551956 C
18.57998109654765 -13.40958568048023 -0.01028264322867 C
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6.99238975005242 9.38889650419404 0.01018123529597 C
4.66942445816832 10.73022469984729 0.01596892428477 C
4.66767523754332 13.41536689488851 0.02498093342981 C
2.34659451442003 14.75374729750557 0.02932151339149 C
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-13.92534496735509 -10.73623164754813 0.03777440130243 C
-16.24240899490235 -9.39087823040052 0.03971902111664 C
-16.24866335594347 -6.71158439878077 0.04219316440738 C
-18.56607436613115 -5.36482318773708 0.04295591350027 C
-18.57022407662064 -2.68731099765057 0.04509190423409 C
-20.88994797246661 -1.33517424888670 0.04277804898084 C
-20.88978625036696 1.33266943321888 0.04291787852488 C
-23.21836627451592 2.70450487214013 0.03585894903904 C
-23.19782862886721 5.33013495599820 0.03371371345388 C
-11.64032273972809 -22.77163940053880 0.01115915464150 C
-13.86940415391146 -21.48452960645214 0.01502776534082 C
-13.94287827178937 -18.77473621915132 0.02304401301909 C
-16.20643726826264 -17.44413581852868 0.02513847957228 C
-16.25951045997595 -14.75902200044161 0.03084954628687 C
-18.53937846949824 -13.40770271952225 0.03099249125201 C
-18.57933718203032 -10.73994015797348 0.03538752690595 C
-20.86957513685626 -9.37125530274323 0.03362309165171 C
-20.89962154329600 -6.72113971988435 0.03730374506769 C
-23.19836258846670 -5.33240814471403 0.03315712568452 C
-23.21862068513432 -2.70678194350826 0.03552676773095 C
-25.52851798119108 -1.28802447569940 0.02763182281201 C
-25.52838492985103 1.28598364520524 0.02783532490532 C
-11.59074743477874 24.77707891388043 -0.00207055884898 H
-15.63049848787903 22.44499757871727 0.00040984411316 H
-6.94540308066862 24.77708272726263 0.00778537837072 H
-2.30018429394712 24.77698701522986 0.01354554184229 H
2.34460212475362 24.77675298120243 0.01498054648190 H
6.98981614929314 24.77638545989041 0.01047133295866 H
11.63514864567720 24.77592617817733 -0.00059419108331 H
15.67467228639966 22.44343307339889 -0.00554839493035 H
17.99735162326968 18.42044292331396 -0.00133080202233 H
20.31987807861223 14.39752412025016 0.00075767028149 H
22.64207342343833 10.37489654749990 0.00121543673874 H
24.96436574768334 6.35183557721443 -0.00080698816161 H
27.28664220260683 2.32861760145338 -0.00578136872665 H
27.28640564820459 -2.33596160759935 -0.00960137478787 H
24.96372431773274 -6.35894471080062 -0.01081022165272 H
20.31841982060585 -14.40417747214308 -0.01437162003127 H
17.99548415384761 -18.42686695608501 -0.01481741044382 H
15.67240208823021 -22.44961809552324 -0.01504494465218 H
11.63264076908928 -24.78170207940770 -0.01131205807999 H
6.98729771174079 -24.78169513478053 -0.00554121039303 H
2.34207629593072 -24.78159117862833 -0.00244471816236 H
-6.94792388368438 -24.78097008369372 0.00143591870114 H
-11.59325572303425 -24.78050549978877 0.00307183887738 H
-15.63277675112430 -22.44801045279661 0.01025313002253 H
-17.95542715007054 -18.42502506940531 0.01944418368576 H
-20.27793013719592 -14.40211610810697 0.02412835896849 H
-22.60012212260829 -10.37950550619836 0.02541308819108 H
-27.24471355908722 -2.33322146149556 0.01842467584446 H
-24.92180552809367 6.35433430909949 0.02483191147934 H
-20.27650298380673 14.39957792447903 0.02231622153851 H
-17.95357304495687 18.42225756406583 0.01417966865466 H
22.64102523397671 -10.38177606637344 -0.01282653219870 H
-2.30271237654611 -24.78134786444018 -0.00066468432950 H
-24.92242630623978 -6.35644775444972 0.02400571974929 H
-22.59910878260334 10.37717801353707 0.02571014278132 H
-27.24448188791929 2.33134552584358 0.01877626642906 H
4.27571474378505 -1.92854948200207 9.94745802440185 N
4.85863257632589 -1.86976812841619 11.77386435287947 H
2.41997661925239 -2.42173187608252 9.97254129755107 H
4.53188129867197 0.54201882289930 8.80305477310553 C
3.10180400437508 2.58147803262171 10.25033240656862 C
1.70252284002797 2.17538275447565 11.99395863899712 O
3.59502480456652 4.91081582322646 9.40273172353399 O
2.64101197107364 6.15144169604561 10.36051515045620 H
6.53940694073007 1.05972961089276 8.80707208579245 H
3.60684313919014 0.48755395354171 6.03553367623200 C
0.79623558975634 0.11581314423023 5.88366583446487 C
-0.24093223813749 -2.29403771457139 5.84928985318257 C
-2.83094211079699 -2.64168158463332 5.81583719831421 C
-4.43914545143533 -0.56757465165303 5.80885193908835 C
-3.41896413800189 1.85508153404960 5.82002566936256 C
-0.83164012890154 2.17804731008809 5.85479160455166 C
-0.06058114066044 4.06926172450655 5.83858398852997 H
-4.68432097650001 3.45280350209968 5.79576231758199 H
-6.99839493428426 -0.81481618645066 5.77227418763592 O
-7.44727356719986 -2.58190479542918 5.74085372355529 H
-3.61086295708159 -4.53297500622820 5.78522163995966 H
0.99207739459520 -3.92144387056497 5.83721740609899 H
4.58691246909114 -1.06321033030212 5.09739729211277 H
4.13984012793008 2.26724282543661 5.14389351386854 H
$end
crest coord -v3 -T 40 -subrmsd -nozs -shake 0 -tstep 1 > crest.out
# for convergence reasons the md settings were adjusted.
# the file .constrains is found automatically
Preparing a Nanoreactor calculation for xtb¶
This is the current workaround for the nanoreactor procedure described in JCTC, 2019, 15, 2847-2862.
Currently there isn’t an automated procedure for the reactor, but the workarounds can already be used with the crest 2.11 version.
The important thing here is mainly a definition of metadynamics parameters and a logfermi potential used for external compression of the system.
There are 3 steps/commands to it (assuming a given input structure is provided as start.xyz):
Generate nano-reactor settings with the command
crest start.xyz --reactor --genpot <density> --genmtd <sim.length>which will produce a file calledrcontrolcontaining the correct xtb constraints.<density>can be the required nano-reactor density in g/cm³ like in the JCTC paper,<sim.length>is the metadynamics length in ps. All other settings, e.g. k and α for the metadynamics, must be directly edited in thercontrolfile. This requires some trial and error but the JCTC paper is generally a good guideline, too.Run the metadynamics with the generated settings using xtb simply with the command
xtb start.xyz --gfn 2 --md --input rcontrol. The trajectory is saved asxtb.trj.To so some (simple) fragment analyzation of
xtb.trjusecrest coord --reactor --fragopt. This will extract all fragments from the trajectory based on neighbor lists, optimize their geometry with xtb and sort them.
Introduction to ENSO¶
What is ENSO ?¶
enso is a utility program to create and refine Conformer, Rotamer-Ensembles and finally prepare all files necessary to generate NMR spectra using the anmr program. enso and additional necessary resources can be found at Github ENSO and Github Cefine.
The Workflow to get the final spectrum is detailed in the following graphic.
NMR spectrum calculation workflow.¶
Short summary¶
The enso program is designed to rerank the Conformer Rotamer Ensemble (CRE) generated by CREST (Conformer Rotamer Ensemble Search Tool) at DFT level and perform subsequent NMR-property calculations. enso interfaces to different QM-CODES (TURBOMOLE, ORCA, xtb) and processes the data. The ENSO is subdivided into four parts.
ENSO flowchart.¶
In part1 crude optimizations are performed at DFT level. Because of crude thresholds only a very small number of optimization cycles are perfomed at DFT level, and the upside is that bondlength are more or less correct. All geometries with a corresponding DFT energy below an energy thresold (thr-part1) are considered for the full optimization in part2.
In part2 the structures are fully optimized at DFT level. On these optimized geometries solvation contributions and thermostatistical contributions to free energy are calculated. The free energy is obtained as the sum of the ‘low-level’ DFT energy \(E\), \(G_{RRHO}\) (thermostatistical contribution to free energy) and \(δG_{solv}\) (optional solvation contribution to free energy). Using a second threshold (this time a free energy based threshold) only conformers with a free energy below the threshold are considered for the final free energy evaluation in part3.
In part3 the ‘high-level’ free energy calculations are performed by calculating high level DFT single-point energies and recalculating the free energy. At this stage Boltzmann weights for the remaining conformers are calculated. All conformers with a Boltzmann contribution below 1% are neglected and the Bolzmann weights are recalculated. The Boltzmann weights are summed up to 98% and all conformers within these 98% are considered for the NMR property calculations.
In part4 the couplings and shieldings calculations are performed. Additionally all information which is required by anmr is written by the enso.
After refining the CREST-ensemble at DFT level and performing the NMR property calculations, anmr correctly averages the shifts and solves the spin hamiltonian for the final spectrum generation. Then anmr generates a file ‘anmr.dat’ which can be plotted to visualize the final spectrum.
Getting started¶
To perform an ENSO calculation first run:
./enso.py [-options]
This generates a ‘flags.dat’ configuration file which stores most information relevant to ENSO.
vim flags.dat # adjust and save the settings in the configuration file to your needs.
After adjusting the settings in the ‘flags.dat’, the input can be automatically checked (for typos and setting-combinations) by enso. This way settings or combinations of settings which are not possible are detected before you actually start the program. The check is performed with:
./enso.py --checkinput
When the input is correct the program can be started by typing:
export PYTHONUNBUFFERED=1
./enso.py --run > enso.out 2> enso.error &
To save the output of enso it is necessary to pipe the output into a file.
Using this export PYTHONUNBUFFERED=1 the progress of the calculations can be
tracked immediatly and the user doesn’t need to wait until the python buffer is
written to the file. For the program to work correctly the information of the
absolute paths to the programs employed in ENSO has to be available in the
global configuration file .ensorc.
Setting up ENSO¶
Contents
Setup¶
Make sure that python3 is installed on your system. Place the program enso.py in your /home/$USER/bin/ folder and add this folder to your PATH. Make the python program executable:
> chmod u+x /home/$USER/bin/enso.py
To setup ENSO place your global configuration file .ensorc in your /home/$USER folder.
If you should not have a global configuration file, you can create it by running:
> enso.py -write_ensorc
This creates the file ensorc_new which you then have to move to your home directory and adjust to your needs:
> mv ensorc_new ~/.ensorc
It is mandatory for enso to find the correct paths to your programs within your global configuration file .ensorc:
> cat ~/.ensorc
.ENSORC
ORCA: /tmp1/orca_4_2_1_linux_x86-64_openmpi216 # here the binary must not be included
ORCA version: 4.2.1
GFN-xTB: /home/path-to/bin/xtb #here the binary has to be included into the path
CREST: /home/path-to/bin/crest #here the binary has to be included into the path
mpshift: /home/path-to/bin/mpshift #here the binary has to be included into the path
escf: /home/path-to/bin/escf #here the binary has to be included into the path
#COSMO-RS
ctd = BP_TZVP_C30_1601.ctd cdir = "/software/cluster/COSMOthermX16/COSMOtherm/ CTDATA-FILES" ldir = "/software/cluster/COSMOthermX16/COSMOtherm/CTDATA-FILES"
cosmothermversion: 16 # 16, 17, 18
$ENDPROGRAMS
#NMR data
reference for 1H: TMS # ('TMS',)
reference for 13C: TMS # ('TMS',)
reference for 19F: CFCl3 # ('CFCl3',)
reference for 31P: TMP # ('TMP', 'PH3')
reference for 29Si: TMS # ('TMS',)
1H active: on # ('on', 'off')
13C active: off # ('on', 'off')
19F active: off # ('on', 'off')
31P active: off # ('on', 'off')
29Si active: off # ('on', 'off')
resonance frequency: None # MHz number of your experimental spectrometer
nconf: all # ('all', 'number e.g. 10')
charge: 0 # number e.g. 0
unpaired: 0 # number e.g. 0
solvent: gas # (acetone, acetonitrile, chcl3, ch2cl2, dmso, h2o, methanol, thf, toluene, gas)
prog: None # ('tm', 'orca')
ancopt: on # ('on', 'off')
prog_rrho: xtb # ('xtb', 'prog', 'off')
gfn_version: gfn2 # ('gfn1', 'gfn2')
temperature: 298.15 # temperature in K e.g. 298.15
prog3: prog # ('tm', 'orca', 'prog')
prog4: prog # ('tm', 'orca', 'prog')
part1: on # ('on', 'off')
part2: on # ('on', 'off')
part3: on # ('on', 'off')
part4: on # ('on', 'off')
boltzmann: off # ('on', 'off')
backup: off # ('on', 'off')
func: pbeh-3c # ('pbeh-3c', 'b97-3c', 'tpss')
func3: pw6b95 # ('pw6b95', 'wb97x', 'dsd-blyp')
basis3: def2-TZVPP # (several basis sets are possible)
funcJ: pbe0 # ('tpss', 'pbe0')
basisJ: def2-TZVP # (several basis sets are possible)
funcS: pbe0 # ('tpss', 'pbe0', 'dsd-blyp')
basisS: def2-TZVP # (several basis sets are possible)
couplings: on # ('on', 'off')
shieldings: on # ('on', 'off')
part1_threshold: 4.0 # number e.g. 4.0
part2_threshold: 2.0 # number e.g. 2.0
sm: default # ('cosmo', 'dcosmors', 'cpcm', 'smd')
smgsolv2: sm # ('sm', 'cosmors', 'gbsa_gsolv')
sm3: default # ('cosmors', 'smd', 'gbsa_gsolv')
sm4: default # ('cosmo', 'cpcm', 'smd')
check: on # ('on', 'off')
crestcheck: off # ('on', 'off')
maxthreads: 1 # number e.g. 2
omp: 1 # number e.g. 4
Requirements¶
ENSO requires:
Python3
External programs which are required:
xtb program version 6.2 or above
crest version 2.6.2 or above
in case of COSMO-RS:
cefine
the TURBOMOLE program package
cosmotherm
in case of TURBOMOLE
cefine
the TURBOMOLE program package
in case of ORCA
ORCA4.1 or above
For the final spectrum generation:
anmr version 3.5 or above
nmrplot.py (needs python3, numpy, matplotlib)
or any other plotting tool (e.g. GNUPLOT)
Detailed information¶
ENSO detailed flowchart.¶
Files written by enso:¶
Files/Folders |
Information |
|---|---|
flags.dat |
The ENSO-run is started from the settings written in this file
|
enso.json |
All information on the conformers is stored in this file
(e.g. energy, boltzmann weight …)
|
populated-conf-part3.xyz |
File containing the geometries of all conformers
remaining in the refined ensemble with energy and
free energy information (thif file was previously called:
‘trj-part3.xyz’
|
conformer_rotamer_check/ |
Folder in which the optimized ensemble (part2) is checked for
rotamers or identical conformers
|
anmr_enso |
File needed by ANMR, containing the Boltzmann weight, free energy
contribution, conformer-folder information
|
.anmrrc |
File needed by ANMR, constaining the reference shieldings, which
nuclei are active, which program package was used for the
NMR property calculations
|
.ensorc |
Global configuration file where the user can adjust
default settings for all ENSO-runs.
and all absolute PATHS to the external programs are stored.
|
CONF# |
folder for conformer # where all calculations concerning
this conformer are performed
|
Settings in .ensorc and flags.dat¶
flags |
explaination |
|---|---|
nconf |
number of conformers considered in this ENSO-run,
taken from the crest_conformers.xyz file
[e.g. 10 or all]
|
charge |
molecular charge
|
unpaired |
number of unpaired electrons
|
solvent |
solvents that are available: gas (if no solvent is required),
[options: gas, acetone, acetonitrile, chcl3, ch2cl2, dmso, h2o,
methanol, thf, toluene]
|
prog |
program- used for calculating part 1 and part 2
[options: tm or orca]
|
ancopt |
if choosen the ANCOPT (Aproximate normal coordinates optimizer)
implemented in
xtb is employed as driver for prog(ORCA, TURBOMOLE) [options: on, off]
|
prog_rrho |
chooses which program is employed for the hessian calculation: either
GFNn-xTB or the program package choosen by prog, our recommendation is
to use GFNn-xTB! In the case that the sorting of the conformers
is supposed to be only based on the energy and not enthalpy the
thermostatistical correction calculations can be turned off and the
sorting is performed only based on energy (then use prog_rrho: off).
[options: prog, xtb, off]
|
gfn_version |
If prog_rrho is set to
xtb then you can choose which GFNn-xTB versionshould be used. We recommend using GFN2-xTB with the keyword gfn2
[options: gfn1, gfn2]
|
prog3 |
The program package for calculating high-level free energies can
be choosen independent of prog [options: prog, tm, orca]
|
prog4 |
The program package for calculating NMR properties can be choosen
independent of the program package chosen for part 1-3.
[options: prog, tm, orca]
|
part1 |
Turn the crude optimization (Part1) on or off, [options: on, off]
|
part2 |
Turn the full optimization and low level free energy calculation
(Part2) on or off [options: on, off]
|
part3 |
Turn the high level free energy calculation on or off (Part3)
[options: on, off]
|
part4 |
Turn the NMR property calculation (Part4) on or off, [options: on, off]
|
boltzmann |
Option to recalculate the boltzmann weight from the data written in
enso.json. [options: on, off]
|
backup |
Option to include conformers which were sorted out either in Part1 or
Part2, because they were above the sorting threshold. This option can be
used after a previous enso-calculation. It can be the case, that conformers
are missing in the final spectrum (because they are high lying in energy at
GFNn-xTB level). The ‘backup’ flag provides an automated way to include
conformers which were just above the respective sorting threshold (in part1
or part2) within the (free) energy window of threshold + 2 kcal/mol. If turned
on in the second run, these higher lying conformers will be optimized and
analyzed in the sorting procedure. [options: on, off]
an example is given in example
|
func |
density functional employed in Part1 and Part2 (crude and full optimization),
[options: pbeh-3c, b97-3c, tpss (tpss is only the keyword, used is the
functional/basis/dispersion correction combination: TPSS-D3/def2-TZVP)]
|
func3 |
density functional for calculating the high level single-point for the high
level free energy evaluation in Part3, [options: pw6b95, wb97x, dsd-blyp]
(Not all functionals are available in each program package (ORCA, TURBOMOLE)!
|
basis3 |
Basis set used for calculating the high level single-point in Part3.
(Be sure that the basis set exists (typos can lead to crashing single-point
calculations). There are more possibilities than mentioned in options, but they
can not be checked!
[options: SVP, SV(P), TZVP, TZVPP, QZVP, QZVPP, def2-SV(P), def2-SVP, def2-TZVP,
def2-TZVPP, def-SVP, def-SV(P), def2-QZVP, DZ, QZV, cc-pVDZ, cc-pVTZ, cc-pVQZ,
cc-pV5Z, aug-cc-pVDZ, aug-cc-pVTZ, aug-cc-pVQZ, aug-cc-pV5Z, def2-QZVPP]
|
couplings |
Option to calculate coupling constants J in Part4 or not (e.g. if you
would want to calculate only shieldings in Part4)
[options: on, off]
|
funcJ |
density functional used to calculate the couplings in the NMR property
calculation = Part4 [options: pbe0, tpss]
|
basisJ |
basis set employed in the calculations of the couplings J in Part4.
[options: e.g. def2-TZVP]
|
shieldings |
Options to calculate shielding constants S in Part4 or not (e.g. if
you would want to calculate only couplings)
[options: on, off]
|
funcS |
density functional used to calculate the shieldings in the NMR property
calculation = Part4 [options: pbe0, tpss]
|
basisS |
basis set employed in the calculations of the shieldings S in Part4.
[options: e.g. def2-TZVP]
|
part1_threshold |
All conformers below this threshold (in kcal/mol) are considered for
the full optimization in Part2.
Conformers within threshold > Econf < (threshold + 2 kcal/mol)
are noted as backup conformers (which can be recalculated if the refined
ensemble is missing some conformers). In Part1 all conformers above
(threshold + 2 kcal/mol) are dismissed. Our recommendation is to
set this threshold to 4.0 kcal/mol.
|
part2_threshold |
All conformers below this threshold (in kcal/mol) are considered for the
high level free energy calculation in Part3. Conformers within
threshold > Econf < (threshold + 2 kcal/mol) are noted as backup conformers.
In Part2 all conformers above (threshold + 2 kcal/mol) are dismissed. Our
recommendation is to set this threshold to 2.0 kcal/mol.
|
sm |
Solvation model employed for the optimization in Part1 und Part2.
Not all solvation models are available in each program package
(ORCA,TURBOMOLE). In order to use the solvation model a solvent has
to be specified! [options: cosmo, dcosmors, cpcm, smd]
|
smgsolv2 |
In Part2 first the full optimization is performed using the solvent
model specified in sm. Then the low level free energy calculation is
performed (still Part2) and to calculate the solvation contribution
to free energy (\(G_{solv}\)) another solvation model can be choosen.
This makes sence, if this solvation model is then used in the high level
free energy calculation Part3 too. [options: sm, cosmors]
|
sm3 |
solvation model employed in the high level free energy calculation Part3.
we recommend to use the same solvation model as in smgsolv2.
[options: cosmors, dcosmors, smd].
|
sm4 |
solvation model employed in the NMR property calculation in Part4.
[options: cosmo, cpcm, smd, dcosmors]
|
check |
Option to terminate the ENSO-run if too many calculations/preparation
steps fail. [options: on, off]
|
crestcheck |
The conformers could become identical or rotamers of each other
during the full DFT optimization (Part2). Therefore we use
CRESTto identify identical conformers or rotamers. The crestcheck option
(on) can automatically remove identical conformers and rotamers.
If it is set to off, the check is still run but the user is only informed
and has to remove the conformers manually after inspection.
Our recommendation is to sort out conformers manually (option: off)
since the sorting alogrithm is threshold based. [options: on, off]
|
maxthreads |
Number of threads the ENSO program can use.
(maxthreads * omp = number of cores)
e.g. the maximal number of calculations that can run in parallel.
Make sure that the number of cores does not exceed your machine
specification.
|
omp |
Number of cores each thread (set with maxthreads)
has available. e.g. maxthreads = 2 and omp = 3 would use two threads
using each three cores, the total number of cores in use would be six.
|
reference for 1H |
Reference for calculating the shifts of your 1H spectrum.
This is written to the file .anmrrc. [options: TMS]
|
reference for 13C |
Reference for calculating the 13C shifts of your spectrum.
This information is written to the file .anmrrc. [options: TMS]
|
1H active |
Calculate NMR properties for the 1H nuclei. [options: on, off]
|
13C active |
Calculate NMR properties for the 13C nuclei [options: on, off]
|
19F active |
Calculate NMR properties for the 19F nuclei [options: on, off]
|
31P active |
Calculate NMR properties for the 31P nuclei [options: on, off]
|
29Si active |
Calculate NMR properties for the 29Si nuclei [options: on, off]
|
resonance frequency |
Frequency of your simulated NMR spectrometer
(the spectrometer you are comparing against.
|
temperature |
Temperature in Kelvin for thermostatistical and Boltzmann weight
evaluation.
|
NMR-property calculations¶
Information about the basis sets employed (default) for NMR property calculations:
def2-TZVP (TURBOMOLE and ORCA)
For user convenience shielding constants of the reference molecules (TMS (Tetramethylsilane), CFCl3, PH3, TMP (Trimethylphosphine oxide)) were precalculated and stored within the enso program. The reference shielding values are used in the anmr program to calculate the shifts and the reference values are written to the file .anmrrc.
To be consistent with your calculation, the reference shielding values were calculated on the reference molecules with many possible geometry-optimization-settings eg. {TURBOMOLE/ORCA, PBEh-3c / TPSS-D3/def2-TZVP / B97-3c, (gas phase or solvent)}. The shieldings were then calculated either with TPSS or PBE0 and depending on ORCA (gas or SMD and def2-TZVP basis set) or TURBOMOLE (gas or DCOSMO-RS with the def2-TZVP basis set). At the end of part4 the file .anmrrc is written into the calculation folder and stores the reference shielding values of your settings for the subsequent ANMR calculation.
Note
The enso program only writes the reference shielding values to the file ‘.anmrrc’ but does not do anything with it. Hence, no results of enso are influenced by a non-matching reference value. If you want to change the reference shielding values, you can simply modify the file ‘.anmrrc’ manually before calling the anmr program.
Procedure for generating the refrence shielding constants: Geometry optimization with of the reference molecule with PBEh-3c/B97-3c/TPSS-D3/def2-TZVP + implicit solvation model (either SMD or DCOSMO-RS). NMR shielding constant calculation with the respective functional and the def2-TZVP basis set (again with implicit solvation model).
Tetramethylsilane:
> cat coord
$coord
2.05833045453195 -2.05833045453195 2.05833045453195 c
3.27901073396930 -3.27901073396930 0.93023223253204 h
3.27901073396930 -0.93023223253204 3.27901073396930 h
0.93023223253204 -3.27901073396930 3.27901073396930 h
-0.00000000000000 0.00000000000000 0.00000000000000 si
-2.05833045453195 2.05833045453195 2.05833045453195 c
-3.27901073396930 3.27901073396930 0.93023223253204 h
-0.93023223253204 3.27901073396930 3.27901073396930 h
-3.27901073396930 0.93023223253204 3.27901073396930 h
2.05833045453195 2.05833045453195 -2.05833045453195 c
0.93023223253204 3.27901073396930 -3.27901073396930 h
3.27901073396930 0.93023223253204 -3.27901073396930 h
3.27901073396930 3.27901073396930 -0.93023223253204 h
-2.05833045453195 -2.05833045453195 -2.05833045453195 c
-3.27901073396930 -3.27901073396930 -0.93023223253204 h
-3.27901073396930 -0.93023223253204 -3.27901073396930 h
-0.93023223253204 -3.27901073396930 -3.27901073396930 h
$end
PH3:
> cat coord
$coord
0.00000000000000 0.00000000000000 1.08780842165939 p
1.12108786201329 1.94178113675579 -0.36261095596909 h
1.12108786201329 -1.94178113675579 -0.36261095596909 h
-2.24217572402658 0.00000000000000 -0.36261095596909 h
$end
TMP = Trimethylphosphine oxide:
> cat coord
$coord
2.10707881159693 -2.37905657209703 -0.95048934768032 c
-0.00002761513490 -0.00001720463363 0.42981024146152 p
0.00022116674358 -0.00003978704989 3.20441724940919 o
-3.11402725504898 -0.63518697865997 -0.95026063129186 c
-4.41578089847492 0.80223353974588 -0.26675109605744 h
-3.74806612133726 -2.46831651344230 -0.26795802048584 h
-3.07053848205114 -0.62555829073221 -3.00039235368914 h
1.00685206250598 3.01430306976026 -0.95039040993479 c
2.90134987179607 3.42432987586201 -0.26440712265899 h
-0.26551500181645 4.47957166601373 -0.27057128439357 h
0.99633316768277 2.97084963842055 -3.00047015163533 h
4.01209383139734 -2.01044112204817 -0.27010522766248 h
1.51433033394466 -4.22477273833643 -0.26505344320048 h
2.07522150306901 -2.34774660838157 -3.00060121737073 h
$end
CFCl3:
> cat coord
$coord
0.00000038126763 -0.00000000884504 0.13419916242803 c
0.00000870296281 0.00000001369727 2.66116007348966 f
3.17274491422955 -0.00000000906271 -0.93176725824334 cl
-1.58637567202181 -2.74767202581384 -0.93179226251812 cl
-1.58637568491745 2.74767203002431 -0.93179224376158 cl
$end
Usage¶
Contents
cis-4-hexen-1-ol¶
Example of calculating the 1H-NMR spectrum of cis-4-hexen-1-ol in CHCl3 at 400 MHz.
> cat coord
$coord
-4.5787202885 -0.8553740252 1.3686940377 C
-3.4023148672 -0.1930996279 -1.1104654057 C
-1.3502307141 1.1896725766 -1.5219716436 C
0.3006494795 2.4620980359 0.3955352829 C
0.2362191223 4.5001215909 0.0503890823 H
3.0642161355 1.6025835718 0.2096773622 C
3.4178595291 -1.1774351958 0.9222138508 C
2.5415191057 -2.8708599609 -0.9480135970 O
0.8099880164 -2.4078504756 -1.3346662145 H
5.4277591776 -1.6058314070 1.1410607567 H
2.4658368243 -1.5681688895 2.7281288136 H
4.2123967195 2.7454371194 1.4856132673 H
3.7614131313 1.8836292778 -1.7127605110 H
-0.3830548458 2.1258051759 2.3091187341 H
-0.7518930894 1.4941446048 -3.4579714157 H
-4.3910561682 -0.9675515200 -2.7291675973 H
-3.5318795176 -0.1003881407 2.9630921609 H
-6.5027613245 -0.1227486813 1.4413316443 H
-4.6902514935 -2.9039535570 1.5605291206 H
$end
Input structure.¶
Start with your (at best already optimized) input structure and create the conformers
and rotamers for the ENSO and ANMR calculation.
> crest coord -gfn2 -g chcl3 -T 4 -nmr > crest.out
In our case CREST found 51 conformers within an energy window of 6 kcal/mol.
We then create a new folder for the ENSO reranking and copy the necessary files:
mkdir enso
cp crest_conformers.xyz coord anmr_nucinfo anmr_rotamer enso/
cd enso/
ENSO requires only the file crest_conformers.xyz, but ANMR needs the last
three files. In the new folder we create the file flags.dat and adapt it to our
choosing. Here we want to calculate everything with TURBOMOLE using PBEh-3c and
DCOSMO-RS for geometry optimization:
enso.py --solvent chcl3 --program tm --programpart4 tm --gfnversion gfn2
--ancoptoptimization on --functional pbeh-3c --solventmodel dcosmors
Tip
You don’t need to give all information using the commandline input and can simply run enso.py without any arguments. This will create the file flags.dat and you can change all information there. But using the commandline input reassures that you don’t have any typos.
> cat flag.dat
FLAGS
nconf: all # all or integer between 0 and total number of conformers
charge: 0 # integer
unpaired: 0 # integer
solvent: chcl3 # acetone, acetonitrile, chcl3, ch2cl2, dmso, h2o, methanol, thf, toluene, gas
prog: tm # tm, orca
ancopt: on # on, off
prog_rrho: xtb # xtb, prog
gfn_version: gfn2 # gfn1, gfn2
temperature: 298.15 # in Kelvin
prog3: tm # tm, orca, prog
prog4: tm # prog, tm, orca
part1: on # on, off
part2: on # on, off
part3: on # on, off
part4: on # on, off
boltzmann: off # on, off
backup: off # on, off
func: pbeh-3c # pbeh-3c, b97-3c, tpss
func3: pw6b95 # pw6b95, wb97x, dsd-blyp
basis3: def2-TZVPP #
couplings: on # on, off
funcJ: pbe0 # tpss, pbe0
basisJ: default #
shieldings: on # on, off
funcS: pbe0 # tpss, pbe0
basisS: default #
part1_threshold: 4.0 # integer or real number
part2_threshold: 2.0 # integer or real number
sm: dcosmors # cosmo, dcosmors, cpcm, smd
smgsolv2: sm # sm, cosmors
sm3: dcosmors # dcosmors, cosmors, smd
sm4: cosmo # cosmo, cpcm, smd
check: on # on, off
crestcheck: off # on, off
maxthreads: 1 # integer larger than 0
omp: 4 # integer larger than 0
reference for 1H: TMS # TMS, DSS
reference for 13C: TMS # TMS, DSS
1H active: on # on, off
13C active: off # on, off
19F active: off # on, off
31P active: off # on, off
resonance frequency: 400 # integer
end
Information on each setting can be found in Settings in .ensorc and flags.dat. Once you have adapted your flags.dat file we can run an input check, testing if the information in flags.dat is correct (no typos and settings combinations are ok {eg. TURBOMOLE doesn’t work with the solvent model SMD}). To do so run:
> enso.py --checkinput
__________________________________________________
| |
| |
| ENSO - |
| energetic sorting of CREST CRE |
| for automated NMR calculations |
| University of Bonn, MCTC |
| July 2018 |
| version 1.26 |
| F. Bohle, K. Schmitz, J. Pisarek and S. Grimme |
| |
|__________________________________________________|
.ensorc is taken from: /home/bohle/.ensorc
Reading absolute paths of programs employed in ENSO.
The following pathways were read in:
ORCA: /tmp1/orca_4_1_0_linux_x86-64_openmpi215
GFN-xTB: /home/abt-grimme/AK-bin/xtb
CREST: /home/bohle/bin/crest
mpshift: /home/bohle/bin/xmpshift
escf: /home/bohle/bin/xescf
Set up of COSMO-RS:
ctd = BP_TZVP_C30_1601.ctd
cdir = "/software/cluster/COSMOthermX16/COSMOtherm/CTDATA-FILES"
ldir = "/software/cluster/COSMOthermX16/COSMOtherm/CTDATA-FILES"
Using /software/cluster/COSMOthermX16/COSMOtherm/DATABASE-COSMO/BP-TZVP-COSMO
as path to the COSMO-RS DATABASE.
Reading user set defaults.
Using conformers from file crest_conformers.xyz.
Using cefine from /home/bohle/bin/cefine
PARNODES for TM or COSMO-RS calculation was set to 4
-----------------------------------------------------------
PARAMETERS
-----------------------------------------------------------
number of atoms in system: 19
number of conformers: 51
charge: 0
unpaired: 0
solvent: chcl3
program for part1 and part2: tm
program for part 3: tm
program for part 4: tm
using ANCOPT implemented in GFN-xTB for the optimization: on
program for RRHO in part 2 and part 3: xtb
temperature: 298.15
GFN-xTB version for RRHO in part 2 and part 3: gfn2
part 1: on
part 2: on
part 3: on
part 4: on
only boltzmann population: off
calculate backup conformers: off
functional for part 1 and 2: pbeh-3c
functional for part 3: pw6b95
basis set for part 3: def2-TZVPP
calculate couplings: on
functional for coupling calculation: pbe0
basis set for coupling calculation: def2-TZVP
calculate shieldings: on
functional for shielding calculation: pbe0
basis set for shielding calculation: def2-TZVP
threshold for part 1: 4.0 kcal/mol
threshold for part 2: 2.0 kcal/mol
solvent model for part 1 and part 2: dcosmors
solvent model for Gsolv contribution of part 2: sm
solvent model for part 3: dcosmors
solvent model for part 4: cosmo
cautious checking for error and failed calculations: on
checking the DFT-ensemble using CREST: off
maxthreads: 1
omp: 4
calculating spectra for: 1H
reference for 1H: TMS
reference for 13C: TMS
reference for 19F: CFCl3
reference for 31P: TMP
resonance frequency: 400
END of parameters
Input check is finished. The ENSO program can be executed with the flag -run.
Please read possible errors at the beginning of the output carefully, they will
hint if your external programs are set up correctly. If you run the ENSO
calculation on a cluster, make sure that all programs are setup correctly in
your jobscript (see Running on a cluster).
Before starting the ENSO calculation, we have to set the number of threads
(maxthreads) (individual calculations e.g. single-points) and number of cores
each thread should have (omp). The total number of cores (maxthreads * omp)
available on your computer is not to be exceeded!
These settings can be written to the global configuration file (if you calculate
always on the same machines) or can be adapted for the individual calculation in
the local configuration file flags.dat.
Tip
When running enso on a cluster it is necessary to source and/or export paths for all employed programs!
Now enso can be run with:
> enso.py -run > enso.out 2> error.enso &
In the following, only parts of the output are shown to highlight important information. During this run in part1 (crude optimization) 49 conformers are within an energy threshold of 4 kcal/mol. These conformers are considered for the full optimization in part2. The two remaining conformers are between 4 and 6 kcal/mol and are considered as backup-confomers. Information of backup conformers is stored in the file enso.json. Since the potential hypersurface between GFNn-xTB and DFT needs not to be parallel, in some cases conformers can be high lying at GFNn-xTB level and low lying at DFT level. To have an automated way of including conformers which would otherwise be disgarded, the ‘backup’ function is introduced and can be activated (after the first enso-run, if it is apparent that dominant conformers are missing) in the local configuration file flags.dat. For this purpose simply restart your enso calculation in the same folder and only change backup: on in the file flags.dat. Then all conformers which are denoted backup-conformers (this information is saved in the file enso.json) will be optimized and evaluated in the sorting procedure.
In part2 first the full DFT optimization is performed and thermostatistical and
solvation contributions are calculated to obtain low-level free energies.
All conformers below a free energy threshold of 2 kcal/mol are considered further.
In this run 35 conformers are considered for part3 and 14 conformers are marked as
backup conformers of part2. After the full optimization at DFT level it is possible
that some conformers could have become rotamers or identical conformers.
This would influence the Boltzmann weights and increase computational cost
unnecessary. To identify them the CREST program is called:
Checking if conformers became rotamers of each other during the DFT-optimization.
The check is performed in the directory conformer_rotamer_check.
Calling CREST to identify rotamers.
WARNING: The following conformers are identified as rotamers or identical.
WARNING: They are NOT sorted out since crestcheck is switched off.
CONFA E(A): G(A):<--> CONFB E(B): G(B):
CONF6 -310.39382 0.43 <--> CONF16 -310.39386 0.34
CONF20 -310.39317 0.50 <--> CONF17 -310.39321 0.96
CONF39 -310.39260 1.08 <--> CONF38 -310.39269 0.96
CONF46 -310.39195 1.70 <--> CONF13 -310.39196 2.03
Since the crestcheck flag is switched off, the conformers are not automatically sorted out and the user has to visually inspect the molecules and sort the conformers as described in Sorting out rotamers at DFT level detected by CREST. We advise you to sort out conformers manually.
In part3 high level DFT single-points are calculated on the 35 conformers passed
from part2. The boltzmann weights are calculated and 24 conformers are considered
for the NMR property calculations in part4. The ‘file populated-conf-part3.xyz’ is written at
the end of part3 and contains all populated conformers. The file ‘anmr_enso’ is written
which is read from ANMR and provides the Boltzmann weights of the populated conformers.
In part4 the couplings and shielding calculations were performed. Finally the file .anmrrc file is written.
At the very end ENSO checks if possible rotamers of each other are in the populated ensemble and notifies the user:
writing .anmrrc
Results are written to enso.json.
***---------------------------------------------------------***
Printing most relevant errors again, just for user convenience:
Possible rotamers of each other still in final ensemble: CONF39 <--> CONF38. Please check by hand!
Possible rotamers of each other still in final ensemble: CONF20 <--> CONF17. Please check by hand!
Possible rotamers of each other still in final ensemble: CONF6 <--> CONF16. Please check by hand!
***---------------------------------------------------------***
END of part4.
-----------------------------------------------------------
ENSO all done!
After inspecting the conformers CONF39 is removed from the ensemble (details on how to do that are shown in Sorting out rotamers at DFT level detected by CREST), because I considered it to be identical to CONF38. After removing the identical conformer we can restart enso.
> enso.py -run > enso.out 2> error.enso &
This time enso will read all necessary information from the file enso.json and
operate with this data. At the end of part3 the Boltzmann weight is recalculated
and two conformers are now additionally populated. For them coupling and shielding
constants are calculated in part4. All files for ANMR are updated.
Now all information is present and ANMR can be called to calculate the full
NMR spectrum:
> anmr > anmr.out 2> error.anmr &
+--------------------------------------+
| A N M R |
| S. Grimme |
| Universitaet Bonn, MCTC |
| 1989-2019 |
| version 3.5 |
| Sat Feb 9 06:41:57 CET 2019 |
+--------------------------------------+
Based on a TurboPascal program written
in 1989 which was translated to F90 in
2005 and re-activated in 2017.
Please cite work employing this code as:
ANMR Ver. 3.5: An automatic, QC based
coupled NMR spectra simulation program.
S. Grimme, Universitaet Bonn, 2019
S. Grimme, C. Bannwarth, S. Dohm, A. Hansen
J. Pisarek, P. Pracht, J. Seibert, F. Neese
Angew. Chem. Int. Ed. 2017, 56, 14763-14769.
DOI:10.1002/anie.201708266
=============================
# OMP threads = 1
=============================
reading <.anmrrc> for standard data
Read TM from anmrrc
1 31.7860000000000 0.000000000000000E+000 1
6 189.674000000000 0.000000000000000E+000 0
9 182.570000000000 0.000000000000000E+000 0
15 291.900000000000 0.000000000000000E+000 0
1H resonance frequency (-mf <real>) : 400.00
line width (-lw <real>) : 1.00
number of all conformers :25
remove J couplings to OH groups : T
maximum spin system size in a fragment :14
fragmentation type (0=none,1=at,2=mol) : 2
chemical shift scalings a,b : 1.00 0.00
spin-spin coupling scal factor : 1.07
plot offset : 0.00
Active nuclei :H
...
SKIPPING A LOT OF OUTPUT
...
=== FRAGMENTED SYSTEM ===
====================================================
solving (J/sigma) averaged spin Hamiltonian
====================================================
spinsystem 1 with 9 spins
1024 product functions 12 Mt blocks, largest is 210
1( 1) 2( 9) 3( 37) 4( 93) 5( 162) 6( 210) 7( 210) 8( 162) 9( 93) 10( 37) 11( 9) 12( 1)
first maxtrix multiply, sparsity in % 99.536 ...
second maxtrix multiply, sparsity in % 94.781 ...
512 product functions 10 Mt blocks, largest is 126
1( 1) 2( 9) 3( 36) 4( 84) 5( 126) 6( 126) 7( 84) 8( 36) 9( 9) 10( 1)
first maxtrix multiply, sparsity in % 99.121 ...
second maxtrix multiply, sparsity in % 91.919 ...
done.
12436 non-zero transitions.
spectrum on <anmr.dat>
Range (delta in ppm) 0.437872924804687 7.03675048828125
Range (delta in Hz) 175.149169921875 2814.70019531250
Min/max Int. ) 4.171584807901128E-003
computing spectrum ...
done.
writing output file ...
done.
All done.
After ANMR finished computing, the file anmr.dat is written and it contains
the spectrum (intensity vs shift) the user can plot:
> nmrplot.py -i anmr.dat exp.dat -start 0 -end 6.5 -o 1Hspectrum -orientation 1 -1
1H NMR spectrum of cis-4-hexen-1-ol in chloroform at 400 MHz, comparing calculated and experimental spectrum. Exp taken from [SDBSWeb : https://sdbs.db.aist.go.jp (National Institute of Advanced Industrial Science and Technology,16-10-2019) (SDBSNo. 11748)].¶
2-methyl-1-pentene¶
Example of calculating the 1H-NMR spectrum of 2-methyl-1-pentene in CHCl3 at 400 MHz.
> cat coord
$coord
-5.1134989926 0.0445408597 0.0007215195 C
-2.3988260553 0.1202192416 0.9598504570 C
-2.0426150350 1.9467776447 1.8509773297 H
-0.4955528936 -0.3025973506 -1.1852527430 C
2.1853738985 -0.2583887206 -0.2367582425 C
3.4286190716 -2.3618737092 0.3005853656 C
2.5901373582 -4.2004809628 0.0485727882 H
5.3374488734 -2.3390838060 1.0097369787 H
3.3398174602 2.3079102171 0.0825121447 C
5.2234930962 2.1788391495 0.8913733279 H
2.1708137054 3.4751040066 1.3098219746 H
3.4682822356 3.2543034689 -1.7427970988 H
-0.7536049204 1.1708293724 -2.6081830586 H
-0.8901990516 -2.1258718566 -2.0673390015 H
-2.1284937554 -1.3401645088 2.3937954454 H
-6.4334377217 0.3509962700 1.5473865797 H
-5.4204111085 1.5054637513 -1.4143993805 H
-5.5276306722 -1.7796998127 -0.8540259276 H
$end
Input structure.¶
Start with your (at best already optimized) input structure and create the conformers
and rotamers for the ENSO and ANMR calculation.
> crest coord -gfn2 -g chcl3 -T 4 -nmr > crest.out
In our case CREST found 6 conformers within an energy window of 6 kcal/mol.
We then create a new folder for the ENSO reranking and copy the necessary files:
mkdir enso
cp crest_conformers.xyz coord anmr_nucinfo anmr_rotamer enso/
cd enso/
ENSO requires only the file crest_conformers.xyz, but ANMR needs the last
three files. In the new folder we create the file flags.dat and adapt it to our
choosing. Here we want to calculate everything with ORCA using PBEh-3c and SMD for
geometry optimization:
enso.py --solvent chcl3 --program orca --programpart4 orca --gfnversion gfn2
--ancoptoptimization on --functional pbeh-3c --solventmodel smd
> cat flag.dat
FLAGS
nconf: all # all or integer between 0 and total number of conformers
charge: 0 # integer
unpaired: 0 # integer
solvent: chcl3 # acetone, acetonitrile, chcl3, ch2cl2, dmso, h2o, methanol, thf, toluene, gas
prog: orca # tm, orca
ancopt: on # on, off
prog_rrho: xtb # xtb, prog
gfn_version: gfn2 # gfn1, gfn2
temperature: 298.15 # in Kelvin
prog3: prog # tm, orca, prog
prog4: prog # prog, tm, orca
part1: on # on, off
part2: on # on, off
part3: on # on, off
part4: on # on, off
boltzmann: off # on, off
backup: off # on, off
func: pbeh-3c # pbeh-3c, b97-3c, tpss
func3: pw6b95 # pw6b95, wb97x, dsd-blyp
basis3: def2-TZVPP #
couplings: on # on, off
funcJ: pbe0 # tpss, pbe0
basisJ: default #
shieldings: on # on, off
funcS: pbe0 # tpss, pbe0
basisS: default #
part1_threshold: 4.0 # integer or real number
part2_threshold: 2.0 # integer or real number
sm: smd # cosmo, dcosmors, cpcm, smd
smgsolv2: sm # sm, cosmors
sm3: smd # dcosmors, cosmors, smd
sm4: cpcm # cosmo, cpcm, smd
check: on # on, off
crestcheck: off # on, off
maxthreads: 3 # integer larger than 0
omp: 4 # integer larger than 0
reference for 1H: TMS # TMS, DSS
reference for 13C: TMS # TMS, DSS
1H active: on # on, off
13C active: off # on, off
19F active: off # on, off
31P active: off # on, off
resonance frequency: 400 # integer
end
After ANMR finished computing, the file anmr.dat is written and it contains
the spectrum (intensity vs shift) the user can plot:
> nmrplot.py -i anmr.dat exp.dat -start 0 -end 6 -o 1Hspectrum -orientation 1 -1
1H NMR spectrum of 2-methly-1-pentene in chloroform at 400 MHz, comparing calculated and experimental spectrum. Exp taken from [SDBSWeb : https://sdbs.db.aist.go.jp (National Institute of Advanced Industrial Science and Technology,16-10-2019) (SDBSNo. 225)].¶
Manually restarting calculations and modifying enso.json¶
In the event that an optimization failes, ENSO discardes the geometry and will not
try to reoptimize the structure. The user can optimize the geometry manually and add the
information on convergence (success) and energy (at the same level as all other calculations)
to the file enso.json. When restarting ENSO the information on the conformers of the previous
run is read from the file enso.json and the manually corrected conformer is further evaluated
within the ongoing enso-run.
Here we show an example on how to manually restart an optimization (part1):
'In case of ORCA using the ANCOPT optimizer implemented in xtb:'
write the geometry in form of a coord file and add at the end of the file:
$external
orca input file = inp
$end
The file 'inp' contains the input for the ORCA program eg.:
%MaxCore 8000
! def2-mSVP pbeh-3c grid4
!ENGRAD
! smallprint printgap noloewdin
%output
print[P_BondOrder_M] 1
print[P_Mayer] 1
print[P_basis] 2
end
%pal
nprocs 7
end
%cpcm
smd true
smdsolvent "chloroform"
end
* xyzfile 0 1 inp.xyz
Then convert the tmole coord file into an xmol file (required by the ORCA input):
> t2x coord > inp.xyz
and then run xtb as driver for ORCA:
> xtb coord --opt crude --orca > opt-part1.out
after convergence convert the optimized geometry back to the coord file!
If the optimization is converged the information has to be written to the enso.json file (to be on the save side, first make a copy of your enso.json file). enso.json contains data on each conformer in the following form:
"plain_uncalculated_CONF":
{
"crude_opt": "not_calculated",
"energy_crude_opt": null,
"backup_for_part2": false,
"consider_for_part2": true,
"opt": "not_calculated",
"energy_opt": null,
"backup_for_part3": false,
"sp_part2": "not_calculated",
"energy_sp_part2": null,
"consider_for_part3": true,
"sp_part3": "calculated",
"energy_sp_part3": null,
"cosmo-rs": "not_calculated",
"energy_cosmo-rs": null,
"gbsa_gsolv": "not_calculated",
"energy_gbsa_gsolv": null,
"rrho": "calculated",
"energy_rrho": null,
"symmetry": "c1",
"consider_for_part4": true,
"1H_J": "not_calculated",
"1H_S": "not_calculated",
"13C_J": "not_calculated",
"13C_S": "not_calculated",
"19F_J": "not_calculated",
"19F_S": "not_calculated",
"31P_J": "not_calculated",
"31P_S": "not_calculated"
"removed_by_user": false
},
"CONF1-example":
{
"crude_opt": "calculated",
"energy_crude_opt": -1034.78500028827,
"backup_for_part2": false,
"consider_for_part2": true,
"opt": "calculated",
"energy_opt": -1034.786028019303,
"backup_for_part3": true,
"sp_part2": "calculated",
"energy_sp_part2": -1034.76193327809,
"consider_for_part3": false,
"sp_part3": "not_calculated",
"energy_sp_part3": null,
"cosmo-rs": "calculated",
"energy_cosmo-rs": -0.028947468366750467,
"gbsa_gsolv": "not_calculated",
"energy_gbsa_gsolv": null,
"rrho": "calculated",
"energy_rrho": 0.369622527533,
"symmetry": "c1",
"consider_for_part4": false,
"1H_J": "not_calculated",
"1H_S": "not_calculated",
"13C_J": "not_calculated",
"13C_S": "not_calculated",
"19F_J": "not_calculated",
"19F_S": "not_calculated",
"31P_J": "not_calculated",
"31P_S": "not_calculated",
"removed_by_user": false
},
Now to change the information on the converged crude optimization (for the conformer CONFX), you have to change:
crude_opt: calculated
energy_crude_opt: eg: -1034.780801227157
Using the updated information, restart your enso-run and the program will automatically evaluate how to proceed with the new information(e.g. sort out this conformer or calculate a full optimization…). You can restart your ENSO-run with:
> enso.py -run > enso.out 2> error.enso &
Note
This procedure is not limited to optimizations, but every failed
calculation can be manually performed. Then the result has to be written to
the file enso.json in the same manner. Then ENSO can restart on the
introduced information.
Sorting out rotamers at DFT level detected by CREST¶
In part2 the conformers are fully optimized at DFT level. It is possible that
during optimization conformers can become rotamers or identical. To identify
these the CREST program is called. If rotamers are found, then ENSO can
sort them out if the crestcheck flag is set. Or the user is simply informed on
the possible existence of these conformers and has to visually inspect the geometries,
decide and adjust the necessary information in the file enso.json (which we recommend).
Here we show which entries to change in the file enso.json:
Note
CREST evaluates conformers to be rotamers or identical based on thresholds concerning the electronic energy, rotational constant and RMSD on the geometries. Visual inspection of possible conformers is encouraged for molecules which show very similar conformers.
To sort out conformers, change the flag consider_for_part3 to false:
"CONFX":
{...
"consider_for_part2": false,
"consider_for_part3": false,
"consider_for_part4": false,
...}
Then set part 1 off within the file 'flags.dat'!
Otherwise consider_for_part_2 will be reset to true ...
Or you can simply set:
"CONFX":
{...
"removed_by_user": true,
...}
This will sort out the conformer.
Running on a cluster¶
When submitting an enso calculation with a jobscript on a computer cluster it is necessary to source and export all programs or paths needed for the enso calculation! An example jobscript looks like:
#!/bin/bash
# PBS Job
#PBS -V
#PBS -N ENSO-Calculation
#PBS -m ae
#PBS -q batch
#PBS -l nodes=1:ppn=14
#
cd $PBS_O_WORKDIR
### setup programs
## XTB
export OMP_NUM_THREADS=1
export MKL_NUM_THREADS=1
ulimit -s unlimited
export OMP_STACKSIZE=1000m
export XTBHOME=/home/$USER/.XTBPARAM/
## TM
export PARA_ARCH=SMP
source /home/path/TURBOMOLE.7.2.1/turbo721
export PARNODES=4
export TM_PAR_FORK=1
## ORCA4.2.1
ORCAPATH="/tmp1/orca_4_2_1_linux_x86-64_openmpi216";
MPIPATH="/software/openmpi-2.1.5/bin";
MPILIB="/software/openmpi-2.1.5/lib64";
PATH=${ORCAPATH}:${MPIPATH}:$PATH
export LD_LIBRARY_PATH=${ORCAPATH}:${MPILIB}:$LD_LIBRARY_PATH
# PATH
PATH=/home/$USER/bin:$PATH
export PATH
### end programs + PATH
export HOSTS_FILE=$PBS_NODEFILE
cat $HOSTS_FILE>hosts_file
TMP_DIR=/tmp1/$USER
DIR1=$PWD
mkdir -p $TMP_DIR/$PBS_JOBID
rsync -q --bwlimit=5000 $DIR1/* $TMP_DIR/$PBS_JOBID/
rsync -q --bwlimit=5000 $DIR1/.* $TMP_DIR/$PBS_JOBID/
rsync -rq --ignore-missing-args --bwlimit=5000 $DIR1/CONF* $TMP_DIR/$PBS_JOBID/
rsync -rq --ignore-missing-args --bwlimit=5000 $DIR1/NMR* $TMP_DIR/$PBS_JOBID/
cd $TMP_DIR/$PBS_JOBID
####################################################################################
#jobs start here (if you have no idea what this script does, only edit this part...)
export PYTHONUNBUFFERED=1
./enso.py -run > enso.out 2> error.enso
#end of job (....and stop editing here.)
#####################################################################################
#copy everything back that is smaller than 5 gbytes
rsync -rq --bwlimit=5000 --max-size=5G $TMP_DIR/$PBS_JOBID/* $DIR1/
rsync -q --bwlimit=5000 --max-size=5G $TMP_DIR/$PBS_JOBID/.* $DIR1/
rsync -rq --bwlimit=5000 --include="*/" --include="mos" --include="alpha" --include="beta" --exclude=* $TMP_DIR/$PBS_JOBID/* $DIR1/
cd $DIR1
rm -r $TMP_DIR/$PBS_JOBID
Tipps¶
Using the def2-QZVP(-gf) basis (only possible with TURBOMOLE and the latest cefine version)! When calculating the high level single-point in part3 the basis def2-QZVP(-gf) basis set can be used. Here all f functions are deleted from hydrogen and all g functions from everything else. This is only supposed to speed up the calculation.
Optimization and sorting the CRE only based on the energy (and not free energy). It is possible to not calculate thermostatistical contributions to free energy, by simply setting the programm for prog_rrho to off. This way all calculations for \(G_{RRHO}\) will be skipped.
Troubleshooting¶
Handling of missing conformers:¶
Use the backup functionallity and make sure that you are not missing a conformer which is high lying in energy at GFNn-xTB level. (See backup)
The conformer might be wrongly sorted into a different conformer group by CREST and counted as a rotamer. To check this you can resort the complete CRE (including all rotamers and conformers) and check if the thresholds employed in the CREGEN sorting routine changes the CRE (See Example applications )
crest coord -cregen crest_rotamers_6.xyz -bthr 12 -nmr > cregen.outHere you have to inspect the printout and check if grouping/sorting of conformers is correct. If you find that there were conformers wrongly grouped because of sorting-thresholds not suitable for the investigated system. You have to rerun the ENSO calculation on the new ensemble file.
Unparallel hypersurfaces between the functional for optimization and high level free energy¶
It is possible that the sorting between the functional/basis used for geometry optimization and the method combination (functional/basis set) for the high level free energy is not parallel. One option is to use a larger basis set for the high level free energy calculation. The default basis set for the single-point calculation in part3 is the def2-TZVP basis. It can be necessary to use a larger basis set. To to so, after the previous run, simply change the basis3 to the basis you desire in the file flags.dat and restart your enso calculation. Be advised that doing so results in the recalculation of all previously calculated single-points in part3!
Influence of the Boltzmann population on the final spectrum¶
The influence of the Boltzmann population on the final spectrum can be checked either by manually adjusting the populations in the file .anmrrc
or by employing different functionals/basis sets
or by checking different solvation models. A quick test, when comparing to additive solvation models (like COSMO-RS) is to use the flag gbsa_gsolv which will calculate a solvation contribution to free energy and performs rather fast.
by verifying that no conformers have become rotamers or identical to each other during DFT optimization (ENSO will inform you on possible cases, but the evaluation should be performed manually)
ANMR¶
ANMR requires the files:
coord, turbomole data group
anmr_nucinfo (human readable), written by crest
information on which nuclei can interchange in your molecule (e.g. the hydrogen atoms in a methlygroup)
= information on chemical and magnetical equivalent atoms
anmr_rotamer (machine readable), written by crest
information on the rotamers detected by crest
anmr_enso, written by enso
information on the contributing conformers, the Boltzmann weight and all contributions to free energy
.anmrrc, written by enso
anmr searches for the .anmrrc file first in the folder of execution and if not found in the home directory of the user
The file contains the reference-shieldings of e.g TMS to convert the calculated shielding to shifts
the folders with the property calculations of the conformers
e.g. CONF1/NMR
Example .anmrrc file:
7 8 XH acid atoms
ENSO qm= TM mf= 300 lw= 1.0 J= on S= on
TMS[chcl3] pbe0[COSMO]/def2-TZVP//pbeh-3c[DCOSMO-RS]/def2-mSVP
1 31.786 0.0 1
6 189.674 0.0 0
9 182.57 0.0 0
15 291.9 0.0 0
The first line in .anmrrc informs anmr to ignore all protons bound to nitrogen
(N=7) and oxygen (O=8). If you want to calculate protons bound to oxygen or nitrogen,
simply remove the corresponding number, but leave the rest of the line intact!
The next line starting with ENSO informs ANMR that the property calculation
was performed by TM = TURBOMOLE (or ORCA = ORCA). The mf= 300 informs ANMR
that the magnetic frequency of the NMR spectrometer is set to 300 MHz. The lw
(linewidth for plotting) is 1.0 and J (couplings) and S (shieldings) are to be evaluated.
If S= off then ANMR will terminate after calculating and averaging the shifts of the
molecule under consideration. The next line explains how the reference shieldings are
calculated: in this case the reference molecule is tetramethylsilane in chloroform and the
shielding is calculated with PBE0/def2-TZVP + COSMO on PBEh-3c + DCOSMO-RS geometries.
The following lines contain the data on [atomic number] [calculated shielding valule of the reference molecule] [experimental shift] [active or not].
The lines show the reference shieldings for hydrogen (1), carbon (6) fluor (9) and phosphorus (15). The third number within the last four lines is 0.0 and can be used to adjust the shift of the reference (e.g. to the experimental shift). The last number in the last four lines can either be 1 or 0 and this switches the ‘element on or off’ for the spectrum calculation.
Example anmr_enso file:
ONOFF NMR CONF BW Energy Gsolv RRHO
1 1 1 0.10042 -354.38939 -0.00899 0.22109
1 2 2 0.32452 -354.39034 -0.00899 0.22093
1 3 3 0.57506 -354.39287 -0.00902 0.22295
The file anmr_enso is written by the enso program and contains information on
the conformers, which folder they are in, the Boltzmann weight, energy, solvation
and thermostatistical contribution to free energy. The first number in the three last
lines indicates to ANMR if the conformer is to be considered (1) or not (0).
If one conformer is not considered (or more) anmr program internally recalculates
the Boltzmann weights based on the free energies from the anmr_enso file.
Usage of anmr:
First of all: the spin problem is of \(2^{N}\) complexity! Depending on the size of the maximalspinsystem (mss) the program might use a lot of RAM! If this is the case, run anmr with a decreased spinsystem size:
anmr -mss 12 > anmr.out 2> anmr.error &
anmr will then write a file called anmr.dat (which is quiet large). The file contains the information ppm vs intesity. This file can then be plotted with any plotting tool or our ‘nmrplot.py’.
To reduce the large size of the file you can remove entries which are close to zero with either this awk or python code:
head -1 anmr.dat > newanmr.dat
awk '($2 > 0.001){print $0}' anmr.dat >> newanmr.dat
tail -1 anmr.dat >> newanmr.dat
import numpy as np
data = np.genfromtxt('anmr.dat')
threshold = 0.001
data2 = data[np.logical_not(data[:,1] < threshold)]
data2 = np.insert(data2, 0, (data[0][0], threshold), axis=0)
data2 = np.insert(data2, len(data2), (data[-1][0], threshold), axis=0)
np.savetxt('newanmr.dat', data2, fmt='%2.5e' )
Spectra Plotting¶
The NMR spectrum can be plotted from the file anmr.dat. It contains the information ppm vs intensity and can be plotted with any plotting tool (e.g GNUPLOT …).
The provided nmrplot.py plotting tool uses matplotlib for plotting. Information on all possible commandline arguments is documented:
> nmrplot.py --help
__________________________________________________
| |
| NMRPLOT |
| Plotting of NMR spectral data |
| University of Bonn, MCTC |
| January 2019 |
| v 1.05 |
| F. Bohle |
|__________________________________________________|
Information on arguments:
End Endremove Startremove Start
+ + + +
+---------------+----+-------------------------------+
lower field higher field
delta /ppm
optional arguments:
-h, --help show this help message and exit
-start START, --startppm START
Start plotting from '<start>' ppm. (default: 0)
-end END, --endppm END
End plotting at '<end>' ppm. Value of end has to be
larger than value of start. (default: 11)
-startremove STARTREMOVE, --startremove STARTREMOVE
Start cutting from spectrum at '<startremove>' ppm.
(default: None)
-endremove ENDREMOVE, --endremove ENDREMOVE
End cutting from spectrum at '<endremove>' ppm. Value
of endremove has to be larger than value of
startremove. (default: None)
-title TITLE, --title TITLE
Set title of entire plot. If no title is required use
'<--title ''>'. (default: NMR-PLOT)
-lw LINEWIDTH, --linewidth LINEWIDTH
Set linewidth. (default: 0.8)
-i FILE [FILE ...], --input FILE [FILE ...]
Provide input_file(s) [max 3 files] -i input1(theory1)
input2(theory2) input3(experiment/predicition);
inputfiles format is two columns: column1 ppm ,
column2 intensity; if several files are provided the
last one will be inverted (default: None)
-l LABEL [LABEL ...], --label LABEL [LABEL ...]
Provide labels for all files provided [max 3 files] -l
label1 label2 label3, if no labels are provided,
filename is used as label (default: [])
-fontsize FONTSIZE, --fontsize FONTSIZE
Set fontsize for entire plot. (default: 15)
-keybox, --keybox Set Frame around key. (default: False)
-ontop, --ontop Plot all spectra ontop of each other. (default: False)
-stacked, --stacked Plot all spectra stacked over each other. (default:
False)
-orientation ORIENTATION [ORIENTATION ...], --orientation ORIENTATION [ORIENTATION ...]
Up (1) or down (-1). (default: [1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1])
-c [ ...], --colors [ ...]
Select colors. Possible are: ['gray', 'blue', 'cyan',
'red', 'green', 'magenta', 'yellow', 'black']
(default: ['blue', 'black', 'red', 'magenta',
'green'])
-cut CUT [CUT ...], --cut CUT [CUT ...]
Cut intensity. Accepts values from 0.0 (flat line) to
1.0 (full intensity). (default: [1.0, 1.0, 1.0, 1.0,
1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0])
-o OUT, --output OUT Provide name of the output file without fileending.
(default: nmrplot)
-s SHIFT [SHIFT ...], --shift SHIFT [SHIFT ...]
Shift ppm of each inputfile separately using: --shift
float float float, e.g. --shift 10.0 0.0 -5.0, each
file needs its own value (default: [])
Introduction to CENSO¶
General information¶
Commandline Energetic SOrting (CENSO) is a sorting algorithm for efficient evaluation of Structure Ensembles (SE). The input ensemble (or single structure) originating from a CREST[SQM/FF] run can be ranked by free energy at DFT level and/or geometries can be optimized using DFT. CENSO has a modular structure, enabling efficient sorting at different levels of theory and targeting individual error sources, e.g., energy or solvation. Sorting is based on (free) energy windows or thresholds, within which all conformers/structures are considered. By choosing appropriate thresholds, the following “properties”/results can be obtained:
lowest lying conformer and corresponding free energy
fully optimized SE and averaged ensemble free energy
Boltzmann populated SE at a given temperature
Apart from the refinement/sorting of SE, CENSO offers an automated approach to calculate NMR properties (shielding and coupling constants) or optical rotatory (OR) dispersion.
To perform fast calculations censo interfaces with QM codes like xtb, crest,
TURBOMOLE and ORCA. The results are read by censo and evaluated in the sorting
algorithm.
The main publication for the CENSO program can be found at J. Phys. Chem. A 2021.
Important
censo always keeps the conformer order of the input ensemble. E.g. CONF35 will
correspond to the 35th conformer of the input ensemble.
CENSO is structured into several parts, which can all be turned on or off by the user. These parts are presented in their intended order:
Part0: Cheap prescreening
Part1: Prescreening
Part2: Optimization (and free energy calculation)
Part3: Refinement (optional at higher hybrid-DFA level)
Part4: NMR-Mode
Part5: OR-Mode
Nomenclature: Free energies (G) are not available in each sorting step, due to the computational cost involved. Sorting-thresholds based on incomplete free energies e.g., without thermostatistical contribution (G_mRRRHO) are denoted by lower case g_thr and full free energies by upper case G_thr.
Parts 0-3 are concerned with efficient SE sorting, optimization and calculation of Boltzmann-weigths for populated structures. The parts are described in the following:
Part0 - Cheap prescreening:¶
Flexible and/or large molecules can have many conformers (i.e., several hundred) and sorting out truly high lying conformers fast is crucial for efficiency. This is the goal of part0. Here the electronic energy description is improved upon the initial SQM/FF energy by performing very fast B97-D3(0)/def2-SV(P)+gcp single-point calculations. If the molecule is in solution phase, solvation is treated at GFN2-xTB[ALPB] level. Sorting is based on g_thr(0) which has to be rather large, e.g. 4 kcal/mol or above.
Part1 - Prescreening:¶
Accurate electronic and solvation energies are calculated in part1. To be efficient COSMO-RS solvation contributions are calculated at r2SCAN-3c level, whereby both the gas phase electronic energy and solvation contribution is obtained and no additional calculations are necessary. Conformers above the threshold g_thr(1) are discarded. After sorting, thermostatistical contributions (G_mRRHO) are calculated at GFN2-xTB[ALPB] level using single-point hessian (Single Point Hessian (SPH) calculations) calculations. Full free energies are calculated and sorting is performed based on G_thr(1). The threshold can be automatically increased (fuzzy-threshold) as a function of the standard deviation of G_mRRHO, which is the case for flexible or diverse SE. Up to now all calculations have been performed on the SQM/FF input geometries!
Part2 - Optimiation:¶
The relevant conformers/structures have to be optimized at DFT (r2SCAN-3c) level in implicit solvation (DCOSMO-RS). An efficient ensemble optimizer has been implemented, where all conformers are optimized for 8 iterations. Then a spearman correlation coefficient is calculated to check for parallel potential energy surfaces. If parallellity can be assumed, the sorting threshold G_thr(2) is decreased and conformers above the threshold are discarded, if their gradient norm is below a predefined threshold. For large ensembles, this decreases the number of high lying conformers fast. The batch wise optimization is repeated until all confomers within the energy window G_thr(2) are fully optimized. On the DFT optimized geometries free energies are calculated like in part1, with COSMO-RS(r2SCAN-3c) for E, dG_solv and GFN2-xTB[ALPB]-SPH for G_mRRHO. Boltzmann weights are calculated and an ensemble averaged free energy can be obtained. The conformers for use in parts 3-5 are considered up to a Boltzmann sum threshold, e.g., all conformers up to 90 % population are further considered.
Part3 - Refinement:¶
If it is necessary to refine the calculated Boltzmann weights at a higher (hybrid) DFT level, this can be performed in part3. Also it has to be noted, that Boltzmann weights calculated from rather accurate r2SCAN-3c energies are reliable enough for most applications. Like in part2 free energy contributions are calculated on DFT optimized geometries, although using a higher (hybrid) DFT level. Conformers below a Boltzmann sum threshold are considered further (e.g. in part4 or part5).
Optional property related parts (part4 and part5) are described below:
Part4 - NMR-Mode:¶
In part4 NMR properties can be calculated for the populated conformers. The Boltzmann weights are taken from either part1, part2 or part3 if they are available. All populated conformers up to the population part2_threshold or part3_threshold are considered. Coupling and shielding constants are calculated separately and can be calculated for the elements H, C, F, Si, P, or all elements. Files for further processing with ANMR are created. After the CENSO run, NMR spectra can be calculated using the ANMR code.
Part5 - OR-Mode:¶
In part5 optical rotatory (OR) dispersion of the populated structure ensemble can be calculated. Boltzmann weights can be taken from part1, part2 or part3.
Setting up CENSO¶
The easiest approach is to download a compiled CENSO binary from the release page:
https://github.com/grimme-lab/CENSO/releases.
There are two versions available censo and censo_w_cefine which contains the latest
cefine version (for TURBOMOLE users). The compiled binaries are created with
pyinstaller and are linked against GLIBC version 2.19 and will work for GLIBC version
2.19 and above.
Next make CENSO executable, create your global configuration file .censorc and adjust settings to your needs.
$ chmod u+x censo_w_cefine
$ mv censo_w_cefine ~/bin/censo
$ cd ~/path_to_project/
$ censo -newconfig
$ mv censorc_new ~/.censorc
$ cat ~/.censorc
# shown in next tab
$CENSO global configuration file: .censorc
$VERSION:1.0.1
ORCA: /path/excluding/binary/
ORCA version: 4.2.1
GFN-xTB: /path/including/binary/xtb-binary
CREST: /path/including/binary/crest-binary
mpshift: /path/including/binary/mpshift-binary
escf: /path/including/binary/escf-binary
#COSMO-RS
ctd = BP_TZVP_C30_1601.ctd cdir = "/software/cluster/COSMOthermX16/COSMOtherm/CTDATA-FILES" ldir = "/software/cluster/COSMOthermX16/COSMOtherm/CTDATA-FILES"
$ENDPROGRAMS
$CRE SORTING SETTINGS:
$GENERAL SETTINGS:
nconf: all # ['all', 'number e.g. 10 up to all conformers']
charge: 0 # ['number e.g. 0']
unpaired: 0 # ['number e.g. 0']
solvent: gas # ['gas', 'acetone', 'acetonitrile', 'aniline', 'benzaldehyde', 'benzene', 'ccl4', '...']
prog_rrho: xtb # ['xtb', 'prog']
temperature: 298.15 # ['temperature in K e.g. 298.15']
trange: [273.15, 378.15, 5] # ['temperature range [start, end, step]']
multitemp: on # ['on', 'off']
evaluate_rrho: on # ['on', 'off']
consider_sym: off # ['on', 'off']
bhess: on # ['on', 'off']
imagthr: automatic # ['automatic or e.g., -100 # in cm-1']
sthr: automatic # ['automatic or e.g., 50 # in cm-1']
scale: automatic # ['automatic or e.g., 1.0 ']
rmsdbias: off # ['on', 'off']
sm_rrho: alpb # ['alpb', 'gbsa']
check: on # ['on', 'off']
prog: tm # ['tm', 'orca']
func: r2scan-3c # ['b97-3c', 'b97-d', 'b97-d3', 'pbe', 'pbeh-3c', 'r2scan-3c', 'tpss']
basis: automatic # ['automatic', 'def2-TZVP', 'def2-mSVP', 'def2-mTZVP', 'def2-mTZVP', '...']
maxthreads: 1 # ['number of threads e.g. 2']
omp: 1 # ['number cores per thread e.g. 4']
cosmorsparam: automatic # ['automatic', '12-fine', '12-normal', '13-fine', '13-normal', '14-fine', '...']
$PART0 - CHEAP-PRESCREENING - SETTINGS:
part0: on # ['on', 'off']
func0: b97-d # ['b97-3c', 'b97-d', 'b97-d3', 'pbe', 'pbeh-3c', 'r2scan-3c', 'tpss']
basis0: def2-SV(P) # ['automatic', 'def2-TZVP', 'def2-mSVP', 'def2-mTZVP', 'def2-mTZVP', '...']
part0_gfnv: gfn2 # ['gfn1', 'gfn2', 'gfnff']
part0_threshold: 4.0 # ['number e.g. 4.0']
$PART1 - PRESCREENING - SETTINGS:
# func and basis is set under GENERAL SETTINGS
part1: on # ['on', 'off']
smgsolv1: cosmors # ['alpb_gsolv', 'cosmo', 'cosmors', 'cosmors-fine', 'cpcm', 'dcosmors', '...']
part1_gfnv: gfn2 # ['gfn1', 'gfn2', 'gfnff']
part1_threshold: 3.5 # ['number e.g. 5.0']
$PART2 - OPTIMIZATION - SETTINGS:
# func and basis is set under GENERAL SETTINGS
part2: on # ['on', 'off']
opt_limit: 2.5 # ['number e.g. 4.0']
sm2: default # ['cosmo', 'cpcm', 'dcosmors', 'default', 'smd']
smgsolv2: cosmors # ['alpb_gsolv', 'cosmo', 'cosmors', 'cosmors-fine', 'cpcm', 'dcosmors', '...']
part2_gfnv: gfn2 # ['gfn1', 'gfn2', 'gfnff']
ancopt: on # ['on']
hlow: 0.01 # ['lowest force constant in ANC generation, e.g. 0.01']
opt_spearman: on # ['on', 'off']
part2_threshold: 99 # ['Boltzmann sum threshold in %. e.g. 95 (between 1 and 100)']
optlevel2: automatic # ['crude', 'sloppy', 'loose', 'lax', 'normal', 'tight', 'vtight', 'extreme', '...']
optcycles: 8 # ['number e.g. 5 or 10']
spearmanthr: -4.0 # ['value between -1 and 1, if outside set automatically']
radsize: 10 # ['number e.g. 8 or 10']
crestcheck: off # ['on', 'off']
$PART3 - REFINEMENT - SETTINGS:
part3: off # ['on', 'off']
prog3: prog # ['tm', 'orca', 'prog']
func3: pw6b95 # ['b97-d3', 'dsd-blyp', 'pbe0', 'pw6b95', 'r2scan-3c', 'wb97x']
basis3: def2-TZVPD # ['DZ', 'QZV', 'QZVP', 'QZVPP', 'SV(P)', 'SVP', 'TZVP', 'TZVPP', 'aug-cc-pV5Z', '...']
smgsolv3: cosmors # ['alpb_gsolv', 'cosmo', 'cosmors', 'cosmors-fine', 'cpcm', 'dcosmors', '...']
part3_gfnv: gfn2 # ['gfn1', 'gfn2', 'gfnff']
part3_threshold: 99 # ['Boltzmann sum threshold in %. e.g. 95 (between 1 and 100)']
$NMR PROPERTY SETTINGS:
$PART4 SETTINGS:
part4: off # ['on', 'off']
couplings: on # ['on', 'off']
progJ: prog # ['tm', 'orca', 'adf', 'prog']
funcJ: pbe0 # ['pbe0', 'pbeh-3c', 'r2scan-3c', 'tpss']
basisJ: def2-TZVP # ['DZ', 'QZV', 'QZVP', 'QZVPP', 'SV(P)', 'SVP', 'TZVP', 'TZVPP', 'aug-cc-pV5Z', '...']
sm4J: default # ['cosmo', 'cpcm', 'dcosmors', 'smd']
shieldings: on # ['on', 'off']
progS: prog # ['tm', 'orca', 'adf', 'prog']
funcS: pbe0 # ['b97-3c', 'dsd-blyp', 'kt1', 'kt2', 'pbe0', 'pbeh-3c', 'r2scan-3c', 'tpss', '...']
basisS: def2-TZVP # ['DZ', 'QZV', 'QZVP', 'QZVPP', 'SV(P)', 'SVP', 'TZVP', 'TZVPP', 'aug-cc-pV5Z', '...']
sm4S: default # ['cosmo', 'cpcm', 'dcosmors', 'smd']
reference_1H: TMS # ['TMS']
reference_13C: TMS # ['TMS']
reference_19F: CFCl3 # ['CFCl3']
reference_29Si: TMS # ['TMS']
reference_31P: TMP # ['TMP', 'PH3']
1H_active: on # ['on', 'off']
13C_active: on # ['on', 'off']
19F_active: off # ['on', 'off']
29Si_active: off # ['on', 'off']
31P_active: off # ['on', 'off']
resonance_frequency: 300.0 # ['MHz number of your experimental spectrometer setup']
$OPTICAL ROTATION PROPERTY SETTINGS:
$PART5 SETTINGS:
optical_rotation: off # ['on', 'off']
funcOR: pbe # ['functional for opt_rot e.g. pbe']
funcOR_SCF: r2scan-3c # ['functional for SCF in opt_rot e.g. r2scan-3c']
basisOR: def2-SVPD # ['basis set for opt_rot e.g. def2-SVPD']
frequency_optical_rot: [589.0] # ['list of freq in nm to evaluate opt rot at e.g. [589, 700]']
$END CENSORC
Upon the first usage of CENSO a folder ~/.censo_assets/ will be created. It contains a file ~/.censo_assets/censo_solvents.json with information on all available solvents and solvent models. If a solvent is not available with a certain solvent model, the user can then choose a replacement solvent, e.g. if benzene is not available choose toluene. This file is directly used in censo and typos will cause the calculation with the repective solvent to crash. For further information see section Solvation.
$ cat ~/.censo_assets/censo_solvents.json
# shown in next tab
# CENSO solvents:
# example:
#{
# "solvent_name_used_in_censo":{
# "solvation_model": ["solvent_name_in_solvation_model", "solvent_name_in_solvation_model_which_is_applied"],
# "solvation_model2": [null _if_solvent_is_not_available, "replacement_solvent_in_solvation_model2"],
# "DC": 20.7 # dielectric constant used for COSMO + DCOSMO-RS
# }
#}
# end example
{
"acetone":{
"cosmors": ["propanone_c0", "propanone_c0"],
"dcosmors": ["propanone", "propanone"],
"xtb": ["acetone", "acetone"],
"cpcm": ["acetone", "acetone"],
"smd": ["ACETONE", "ACETONE"],
"DC": 20.7
},
"chcl3":{
"cosmors": ["chcl3_c0", "chcl3_c0"],
"dcosmors": ["chcl3", "chcl3"],
"xtb": ["chcl3", "chcl3"],
"cpcm": ["chloroform","chloroform"],
"smd": ["CHLOROFORM", "CHLOROFORM"],
"DC": 4.8
},
"acetonitrile":{
"cosmors": ["acetonitrile_c0", "acetonitrile_c0"],
"dcosmors": ["acetonitrile", "acetonitrile"],
"xtb": ["acetonitrile", "acetonitrile"],
"cpcm": ["acetonitrile", "acetonitrile"],
"smd": ["ACETONITRILE", "ACETONITRILE"],
"DC": 36.6
},
"ch2cl2":{
"cosmors": ["ch2cl2_c0", "ch2cl2_c0"],
"dcosmors": [null, "chcl3"],
"xtb": ["ch2cl2", "ch2cl2"],
"cpcm": ["CH2Cl2", "CH2Cl2"],
"smd": ["DICHLOROMETHANE", "DICHLOROMETHANE"],
"DC": 9.1
},
"dmso":{
"cosmors": ["dimethylsulfoxide_c0", "dimethylsulfoxide_c0"],
"dcosmors": ["dimethylsulfoxide", "dimethylsulfoxide"],
"xtb": ["dmso", "dmso"],
"cpcm": ["DMSO", "DMSO"],
"smd": ["DIMETHYLSULFOXIDE", "DIMETHYLSULFOXIDE"],
"DC": 47.2
},
"h2o":{
"cosmors": ["h2o_c0", "h2o_c0"],
"dcosmors": ["h2o", "h2o"],
"xtb": ["h2o", "h2o"],
"cpcm": ["Water", "Water"],
"smd": ["WATER", "WATER"],
"DC": 80.1
},
"methanol":{
"cosmors": ["methanol_c0", "methanol_c0"],
"dcosmors": ["methanol", "methanol"],
"xtb": ["methanol", "methanol"],
"cpcm": ["Methanol", "Methanol"],
"smd": ["METHANOL", "METHANOL"],
"DC": 32.7
},
"thf":{
"cosmors": ["thf_c0", "thf_c0"],
"dcosmors": ["thf", "thf"],
"xtb": ["thf", "thf"],
"cpcm": ["THF", "THF"],
"smd": ["TETRAHYDROFURAN", "TETRAHYDROFURAN"],
"DC": 7.6
},
"toluene":{
"cosmors": ["toluene_c0", "toluene_c0"],
"dcosmors": ["toluene", "toluene"],
"xtb": ["toluene", "toluene"],
"cpcm": ["Toluene", "Toluene"],
"smd": ["TOLUENE", "TOLUENE"],
"DC": 2.4
},
"octanol":{
"cosmors": ["1-octanol_c0", "1-octanol_c0"],
"dcosmors": ["octanol", "octanol"],
"xtb": ["octanol", "octanol"],
"cpcm": ["Octanol", "Octanol"],
"smd": ["1-OCTANOL", "1-OCTANOL"],
"DC": 9.9
},
"woctanol":{
"cosmors": [null, "woctanol"],
"dcosmors": ["wet-otcanol", "wet-octanol"],
"xtb": ["woctanol", "woctanol"],
"cpcm": [null, "Octanol"],
"smd": [null, "1-OCTANOL"],
"DC": 8.1
},
"hexadecane":{
"cosmors": ["n-hexadecane_c0", "n-hexadecane_c0"],
"dcosmors": ["hexadecane", "hexadecane"],
"xtb": ["hexadecane", "hexadecane"],
"cpcm": [null, "Hexane"],
"smd": ["N-HEXADECANE", "N-HEXADECANE"],
"DC": 2.1
},
"dmf":{
"cosmors": ["dimethylformamide_c0","dimethylformamide_c0"],
"dcosmors": [null, "dimethylsulfoxide"],
"xtb": ["dmf", "dmf"],
"cpcm": ["DMF", "DMF"],
"smd": ["N,N-DIMETHYLFORMAMIDE", "N,N-DIMETHYLFORMAMIDE"],
"DC": 38.3
},
"aniline":{
"cosmors": ["aniline_c0", "aniline_c0"],
"dcosmors": ["aniline", "aniline"],
"xtb": ["aniline", "aniline"],
"cpcm": [null,"Pyridine"],
"smd": ["ANILINE", "ANILINE"],
"DC": 6.9
},
"cyclohexane":{
"cosmors": ["cyclohexane_c0", "cyclohexane_c0"],
"dcosmors": ["cyclohexane", "cyclohexane"],
"xtb": [null, "hexane"],
"cpcm": ["Cyclohexane", "Cyclohexane"],
"smd": ["CYCLOHEXANE", "CYCLOHEXANE"],
"DC": 2.0
},
"ccl4":{
"cosmors": ["ccl4_c0", "ccl4_c0"],
"dcosmors": ["ccl4", "ccl4"],
"xtb": ["ccl4", "ccl4"],
"cpcm": ["CCl4", "CCl4"],
"smd": ["CARBON TETRACHLORIDE", "CARBON TETRACHLORIDE"],
"DC": 2.2
},
"diethylether":{
"cosmors": ["diethylether_c0", "diethylether_c0"],
"dcosmors": ["diethylether", "diethylether"],
"xtb": ["ether", "ether"],
"cpcm": [null, "THF"],
"smd": ["DIETHYL ETHER", "DIETHYL ETHER"],
"DC": 4.4
},
"ethanol":{
"cosmors": ["ethanol_c0", "ethanol_c0"],
"dcosmors": ["ethanol", "ethanol"],
"xtb": ["ethanol", "ethanol"],
"cpcm": [null, "Methanol"],
"smd": ["ETHANOL", "ETHANOL"],
"DC": 24.6
},
"hexane":{
"cosmors": ["hexane_c0", "hexane_c0"],
"dcosmors": ["hexane", "hexane"],
"xtb": ["hexane", "hexane"],
"cpcm": ["Hexane", "Hexane"],
"smd": ["N-HEXANE", "N-HEXANE"],
"DC": 1.9
},
"nitromethane":{
"cosmors": ["nitromethane_c0", "nitromethane_c0"],
"dcosmors": ["nitromethane", "nitromethane"],
"xtb": ["nitromethane", "nitromethane"],
"cpcm": [null, "methanol"],
"smd": "",
"DC": 38.2
},
"benzaldehyde":{
"cosmors": ["benzaldehyde_c0", "benzaldehyde_c0"],
"dcosmors": [null, "propanone"],
"xtb": ["benzaldehyde", "benzaldehyde"],
"cpcm": [null, "Pyridine"],
"smd": ["BENZALDEHYDE", "BENZALDEHYDE"],
"DC": 18.2
},
"benzene":{
"cosmors": ["benzene_c0", "benzene_c0"],
"dcosmors": [null, "toluene"],
"xtb": ["benzene", "benzene"],
"cpcm": ["Benzene", "Benzene"],
"smd": ["BENZENE", "BENZENE"],
"DC": 2.3
},
"cs2":{
"cosmors": ["cs2_c0", "cs2_c0"],
"dcosmors": [null, "ccl4"],
"xtb": ["cs2", "cs2"],
"cpcm": [null, "CCl4"],
"smd": ["CARBON DISULFIDE", "CARBON DISULFIDE"],
"DC": 2.6
},
"dioxane":{
"cosmors": ["dioxane_c0", "dioxane_c0"],
"dcosmors": [null, "diethylether"],
"xtb": ["dioxane", "dioxane"],
"cpcm": [null, "Cyclohexane"],
"smd": ["1,4-DIOXANE", "1,4-DIOXANE"],
"DC": 2.2
},
"ethylacetate":{
"cosmors": ["ethylacetate_c0", "ethylacetate_c0"],
"dcosmors": [null, "diethylether"],
"xtb": ["ethylacetate", "ethylacetate"],
"cpcm": [null, "THF"],
"smd": ["ETHYL ETHANOATE", "ETHYL ETHANOATE"],
"DC": 5.9
},
"furan":{
"cosmors": ["furane_c0", "furane_c0"],
"dcosmors": [null, "diethylether"],
"xtb": ["furane", "furane"],
"cpcm": [null, "THF"],
"smd": [null, "THF"],
"DC": 3.0
},
"phenol":{
"cosmors": ["phenol_c0", "phenol_c0"],
"dcosmors": [null, "thf"],
"xtb": ["phenol", "phenol"],
"cpcm": [null, "THF"],
"smd": [null, "THIOPHENOL"],
"DC": 8.0
}
}
Get additional Information:¶
Some information is already contained in censo and can be accessed by running:
$ censo --help
# explaination of all possible command line arguments
# shown in next tab
______________________________________________________________
| |
| |
| CENSO - Commandline ENSO |
| v 1.0.1 |
| energetic sorting of CREST Conformer Rotamer Ensembles |
| University of Bonn, MCTC |
| Feb 2021 |
| based on ENSO version 2.0.1 |
| F. Bohle and S. Grimme |
| |
|______________________________________________________________|
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
optional arguments:
-h, --help show this help message and exit
GENERAL SETTINGS:
-inp , --input Input name of ensemble file: e.g. crest_conformers.xyz
-nc , --nconf Number of conformers which are going to be considered
(max number of conformers are all conformers from the
input file).
-chrg , --charge Charge of the investigated molecule.
-u , --unpaired Integer number of unpaired electrons of the
investigated molecule.
-T , --temperature Temperature in Kelvin for thermostatistical
evaluation.
-multitemp , --multitemp
Needs to be turned on if a temperature range should be
evaluated (flag trange). Options for multitemp are:
['on' or 'off'].
-trange start end step, --trange start end step
specify a temperature range [start, end, step] e.g.:
250.0 300.0 10.0 resulting in [250.0, 260.0, 270.0,
280.0, 290.0].
-bhess , --bhess Applies structure constraint to input/DFT geometry for
mRRHO calcuation.Options are: ['on' or 'off'].
-consider_sym , ---consider_sym
Consider symmetry in mRRHO calcuation (based on desy
xtb threshold).Options are: ['on' or 'off'].
-rmsdbias , --rmsdbias
Applies constraint to rmsdpot.xyz to be consistent to
CREST.Options are: ['on' or 'off'].
-sm_rrho , --sm_rrho
Solvation model used in xTB GmRRHO calculation.
Applied if not in gas-phase. Options are 'gbsa' or
'alpb'.
-evaluate_rrho , --evaluate_rrho
Evaluate mRRHO contribution. Options: on or off.
-func , --functional
Functional for geometry optimization (used in part2)
and single-points in part1
-basis , --basis Basis set employed together with the functional (func)
for the low level single point in part1 und
optimization in part2.
-checkinput, --checkinput
Option to check if all necessary information for the
ENSO calculation are provided and check if certain
setting combinations make sence. Option to choose from
: ['on' or 'off']
-solvent , --solvent
Solvent the molecule is solvated in, available
solvents are: ['gas', 'acetone', 'acetonitrile',
'aniline', 'benzaldehyde', 'benzene', 'ccl4',
'ch2cl2', 'chcl3', 'cs2', 'cyclohexane',
'diethylether', 'dioxane', 'dmf', 'dmso', 'ethanol',
'ethylacetate', 'furan', 'h2o', 'hexadecane',
'hexane', 'methanol', 'nitromethane', 'octanol',
'phenol', 'thf', 'toluene', 'woctanol']. They can be
extended in the file
~/.censo_assets/censo_solvents.json .
-prog , --prog QM-program used in part1 and part2 either 'orca' or
'tm'.
-prog_rrho , --prog_rrho
QM-program for mRRHO contribution in part1 2 and 3,
either 'xtb' or 'prog'.
-crestcheck , --crestcheck
Option to sort out conformers after DFT optimization
which CREST identifies as identical or rotamers of
each other. The identification/analysis is always
performed, but the removal of conformers has to be the
choice of the user. Options are: ['on' or 'off']
-check {on,off}, --check {on,off}
Option to terminate the ENSO-run if too many
calculations/preparation steps fail. Options are:
['on' or 'off'].
-version, --version Print CENSO version and exit.
-part3only, --part3only
Option to turn off part1 and part2
-cosmorsparam , --cosmorsparam
Choose a COSMO-RS parametrization for possible COSMO-
RS G_solv calculations: e.g. 19-normal for
'BP_TZVP_19.ctd' or 16-fine for
'BP_TZVPD_FINE_C30_1601.ctd'.
SPECIAL RUN MODES:
-logK, --logK Automatically set required settings for logK
calculation. Of course charge, solvent etc. has to be
set by the user.
CRE CHEAP-PRESCREENING - PART0:
-part0 , --part0 Option to turn the CHEAP prescreening evaluation
(part0) which improves description of ΔE 'on' or
'off'.
-func0 , --func0 Functional for fast single-point (used in part0)
-basis0 , --basis0 Basis set employed together with the functional
(func0) for the fast single point calculation in
part0.
-part0_gfnv , --part0_gfnv
GFNn-xTB version employed for calculating the gas
phase GFNn-xTB single point in part0. Allowed values
are [gfn1, gfn2, gfnff]
-part0_threshold , -thrpart0 , --thresholdpart0
Threshold in kcal/mol. All conformers in part0 (cheap
single-point) with a relativ energy below the
threshold are considered for part1.
CRE PRESCREENING - PART1:
-part1 , --part1 Option to turn the prescreening evaluation (part1)
'on' or 'off'.
-smgsolv1 , --smgsolv1
Solvent model for the Gsolv evaluation in part1. This
can either be an implicit solvation or an additive
solvation model. Allowed values are [alpb_gsolv,
cosmo, cosmors, cosmors-fine, cpcm, dcosmors,
gbsa_gsolv, sm2, smd, smd_gsolv]
-part1_gfnv , --part1_gfnv
GFNn-xTB version employed for calculating the mRRHO
contribution in part1. Allowed values are [gfn1, gfn2,
gfnff]
-part1_threshold , -thrpart1 , --thresholdpart1
Threshold in kcal/mol. All conformers in part1
(lax_single-point) with a relativ energy below the
threshold are considered for part2.
CRE OPTIMIZATION - PART2:
-part2 , --part2 Option to turn the full optimization (part2) 'on' or
'off'.
-sm2 , --solventmodel2
Solvent model employed during the geometry
optimization part2.The solvent model sm2 is not used
for Gsolv evaluation, but for the implicit effect on a
property (e.g. the optimization).
-smgsolv2 , --smgsolv2
Solvent model for the Gsolv calculation in part2.
Either the solvent model of the optimization (sm) or
an additive solvation model. Allowed values are
[alpb_gsolv, cosmo, cosmors, cosmors-fine, cpcm,
dcosmors, gbsa_gsolv, sm2, smd, smd_gsolv]
-part2_gfnv , --part2_gfnv
GFNn-xTB version employed for calculating the mRRHO
contribution in part2. Allowed values are [gfn1, gfn2,
gfnff]
-ancopt Option to use xtb as driver for the xTB-optimizer in
part2.
-opt_spearman Option to use an optimizer which checks if the
hypersurface of DFT andxTB is parallel and optimizes
mainly low lying conformers
-optlevel2 , --optlevel2
Option to set the optlevel in part2, only if
optimizing with the xTB-optimizer!Allowed values are
crude, sloppy, loose, lax, normal, tight, vtight,
extreme, automatic
-optcycles , --optcycles
number of cycles in ensemble optimizer.
-hlow , --hlow Lowest force constant in ANC generation (real), used
by xTB-optimizer.
-spearmanthr , --spearmanthr
Value between -1 and 1 for the spearman correlation
coeffient threshold
-opt_limit , --opt_limit
Lower limit Threshold in kcal/mol. If the GFNn and DFT
hypersurfaces areassumed parallel, the conformers
above the threshold are removed and not optimized
further.The conformers in part2 with a relativ free
energy below the threshold are fully optimized.
-thrpart2 , --thresholdpart2 , -part2_threshold
Boltzmann population sum threshold for part2 in %. The
conformers with the highest Boltzmann weigths are
summed up until the threshold is reached.E.g. all
conformers up to a Boltzmann population of 90 % are
considered.Example usage: "-thrpart2 99" --> considers
a population of 99 %
-radsize , --radsize
Radsize used in optimization and only for r2scan-3c!
CRE REFINEMENT - PART3:
-part3 , --part3 Option to turn the high level free energy evaluation
(part3) 'on' or 'off'.
-prog3 , --prog3 QM-program used in part3 either 'orca' or 'tm'.
-func3 , --functionalpart3
Functional for the COSMO-RS calculation, use
functional names as recognized by cefine.
-basis3 , --basis3 Basis set employed together with the functional
(func3) for the high level single point in part3.
-smgsolv3 , --smgsolv3
Solvent model for the Gsolv calculation in part3.
Either the solvent model of the optimization (sm2) or
an additive solvation model.
-part3_gfnv , --part3_gfnv
GFNn-xTB version employed for calculating the mRRHO
contribution in part3. Allowed values are [gfn1, gfn2,
gfnff]
-thrpart3 , --thresholdpart3
Boltzmann population sum threshold for part3 in %. The
conformers with the highest Boltzmann weigths are
summed up until the threshold is reached.E.g. all
conformers up to a Boltzmann population of 90 % are
consideredExample usage: "-thrpart3 99" --> considers
a population of 99 %
NMR Mode:
-part4 , --part4 Option to turn the NMR property calculation mode
(part4) 'on' or 'off'.
-couplings , --couplings
Option to run coupling constant calculations. Options
are 'on' or 'off'.
-prog4J , --prog4J QM-program for the calculation of coupling constants.
-funcJ , --funcJ Functional for the coupling constant calculation.
-basisJ , --basisJ Basis set for the calculation of coupling constants.
-sm4_j , --sm4_j Solvation model used in the coupling constant
calculation.
-shieldings , --shieldings
Option to run shielding constant calculations. Options
are 'on' or 'off'.
-prog4S , --prog4S QM-program for the calculation of shielding constants.
-funcS , --funcS Functional for shielding constant calculation.
-basisS , --basisS Basis set for the calculation of shielding constants.
-sm4_s , --sm4_s Solvation model used in the shielding constant
calculation.
-hactive , --hactive
Investigates hydrogen nuclei in coupling and shielding
calculations.choices=['on', 'off']
-cactive , --cactive
Investigates carbon nuclei in coupling and shielding
calculations.choices=['on', 'off']
-factive , --factive
Investigates fluorine nuclei in coupling and shielding
calculations.choices=['on', 'off']
-siactive , --siactive
Investigates silicon nuclei in coupling and shielding
calculations.choices=['on', 'off']
-pactive , --pactive
Investigates phosophorus nuclei in coupling and
shielding calculations.choices=['on', 'off']
OPTICAL ROTATION MODE:
-OR , --OR , -part5 Do optical rotation calculation.
-funcOR , --funcOR Functional for optical rotation calculation.
-funcOR_SCF , --funcOR_SCF
Functional used in SCF for optical rotation
calculation.
-basisOR , --basisOR
Basis set for optical rotation calculation.
-freqOR [ [ ...]], --freqOR [ [ ...]]
Frequencies to evaluate specific rotation at in nm.
E.g. 589 Or 589 700 to evaluate at 598 nm and 700 nm.
OPTIONS FOR PARALLEL CALCULATIONS:
-O , --omp Number of cores each thread can use. E.g. (maxthreads)
5 threads with each (omp) 4 cores --> 20 cores need to
be available on the machine.
-P , --maxthreads Number of independent calculations during the ENSO
calculation. E.g. (maxthreads) 5 independent
calculation- threads with each (omp) 4 cores --> 20
cores need to be available on the machine.
Concerning overall mRRHO calculations:
-imagthr , --imagthr
threshold for inverting imaginary frequencies for
thermo in cm-1. (e.g. -30.0)
-sthr , --sthr Rotor cut-off for thermo in cm-1. (e.g. 50.0)
-scale , --scale scaling factor for frequencies (e.g. 1.0)
CREATION/DELETION OF FILES:
--cleanup, -cleanup Delete unneeded files from current working directory.
--cleanup_all, -cleanup_all
Delete all unneeded files from current working
directory. Stronger than -cleanup !
-newconfig, -write_censorc, --write_censorc
Write new configuration file, which is placed into the
current directory.
-inprc INPRCPATH, --inprc INPRCPATH
Path to the destination of the configuration file
.censorc
-tutorial, --tutorial
Start interactive CENSO documentation.
$ censo -tutorial
# general explainations
# shown in next tab
______________________________________________________________
| |
| |
| CENSO - Commandline ENSO |
| v 1.0.1 |
| energetic sorting of CREST Conformer Rotamer Ensembles |
| University of Bonn, MCTC |
| Feb 2021 |
| based on ENSO version 2.0.1 |
| F. Bohle and S. Grimme |
| |
|______________________________________________________________|
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
This is the CENSO tutorial / interactive documentation:
Topic options are:
general
censorc
setup
thresholds
solvation
examples
files
jobscript
everything
To exit please type one of the following: exit or q
Please input your information request:
....
Requirements¶
CENSO needs other programs in certain versions and will not work properly without them:
xTB in version 6.4.0 or above
TM in version 7.5.x or above (when using r2scan-3c)
ORCA in version 4.x or above
cefine in the newest version, when using TURBOMOLE (or use censo_w_cefine)
Run CENSO on a cluster¶
When submitting a calculation on a cluster architecture the following points have to be considered:
Are the program paths in your .censorc file correct (ORCA, xTB, CREST, COSMO-RS)
Is the correct TURBOMOLE version sourced in your job-submission file and are the correct environment variables for parallelization set?
provide the correct number of available cores to CENSO (P, maxthreads) * (O,omp) = number of cores
CENSO will generate a lot of data for each conformer. This data is stored in the CONFX (X=number) folders. If you restart and resubmit a calculation to the cluster, you have to tell your submission script to copy these folders.
Hint
CENSO can not be parallelized over several nodes!
Example job-submission script
#!/bin/bash
# PBS Job
#PBS -V
#PBS -N JOB_NAME
#PBS -m ae
#PBS -q batch
#PBS -l nodes=1:ppn=28
#
cd $PBS_O_WORKDIR
### setup programs
## XTB
export OMP_NUM_THREADS=1
export MKL_NUM_THREADS=1
ulimit -s unlimited
export OMP_STACKSIZE=1000m
## TM
export PARA_ARCH=SMP
source /home/$USER/bin/.turbo751
export PARNODES=4 ## omp
export TM_PAR_FORK=1
### ORCA4.2.1
ORCAPATH="/tmp1/orca_4_2_1_linux_x86-64_openmpi216";
MPIPATH="/software/openmpi-2.1.5/bin";
MPILIB="/software/openmpi-2.1.5/lib64";
PATH=${ORCAPATH}:${MPIPATH}:$PATH
LD_LIBRARY_PATH=${ORCAPATH}:${MPILIB}:$LD_LIBRARY_PATH
LD_LIBRARY_PATH=/software/intel/parallel_studio_xe_2017.1/parallel_studio_xe_2017.4.056/compilers_and_libraries_2017/linux/compiler/lib/intel64_lin:$LD_LIBRARY_PATH
LD_LIBRARY_PATH=/software/intel/parallel_studio_xe_2017/mkl/lib/intel64:$LD_LIBRARY_PATH
export LD_LIBRARY_PATH
## PATH
PATH=/home/$USER/bin:$PATH
export PATH
### end programs + PATH
export HOSTS_FILE=$PBS_NODEFILE
cat $HOSTS_FILE>hosts_file
TMP_DIR=/tmp1/$USER
DIR1=$PWD
mkdir -p $TMP_DIR/$PBS_JOBID
#check file system access
if [ ! -d $TMP_DIR/$PBS_JOBID ]; then
echo "Unable to create $TMP_DIR/$PBS_JOBID on $HOSTNAME. Must stop."
exit
fi
#check current location
if [ "$PWD" == "$HOME" ]; then
echo "Cowardly refusing to copy the whole home directory"
exit
fi
#copy everything to node (will NOT copy directories for safety reasons.
#Add an 'r' only if absolutely sure what you are doing)
#bwlimit limits bandwidth to 5000 kbytes/sec
rsync -q --bwlimit=5000 $DIR1/* $TMP_DIR/$PBS_JOBID/
rsync -rq --ignore-missing-args --bwlimit=5000 $DIR1/CONF* $TMP_DIR/$PBS_JOBID/
rsync -q --bwlimit=5000 $DIR1/.* $TMP_DIR/$PBS_JOBID/
cd $TMP_DIR/$PBS_JOBID
####################################################################################
#Gettimings
start=$(date +%s)
#####################################################################################
#jobs start here (if you have no idea what this script does, only edit this part...)
echo "Calculation from $(date)" >> RUNTIME
export PYTHONUNBUFFERED=1
censo -inp inputfile.xyz -P 7 -O 4 > censo.out
#end of job (....and stop editing here.)
#####################################################################################
#Print timings to file
end=$(date +%s)
secs=$(expr $end - $start)
printf '%dh:%dm:%02ds\n' $(($secs/3600)) $(($secs%3600/60)) $(($secs%60)) >> RUNTIME
#####################################################################################
#copy everything back that is smaller than 5 gbytes
rsync -rq --bwlimit=5000 --max-size=5G $TMP_DIR/$PBS_JOBID/* $DIR1/
rsync -q --bwlimit=5000 --max-size=5G $TMP_DIR/$PBS_JOBID/.* $DIR1/
#to be safe, get mos alpha and beta seperately.
#Note that the rsync syntax is strange; you need to first include everything,
#then exclude the rest ("*" includes subdirectories)
rsync -rq --bwlimit=5000 --include="*/" --include="mos" --include="alpha" --include="beta" --exclude=* $TMP_DIR/$PBS_JOBID/* $DIR1/
#if you want the large files as well, comment in the following
#rsync -r --bwlimit=1000 --min-size=5G $TMP_DIR/$PBS_JOBID/* $DIR1/
cd $DIR1
rm -r $TMP_DIR/$PBS_JOBID
Censorc keyword definitions¶
Contents
General Settings¶
keyword |
definition |
|---|---|
nconf |
how many conformers should be considered. Either a number or the flag all. |
charge |
molecular charge of the molecule under investigation. |
unpaired |
number of unpaired electrons in the molecule under investigation. |
solvent |
Solvent if the molecule is in solution phase, else gas. |
prog_rrho |
QM-code used for the calculation of thermostatistical contributions. This is only feasible with xtb, since normally a large number of hessian calculations have to be performed. |
temperature |
Temperature (in Kelvin) used for the Boltzmann evaluations. |
trange |
temperature range which is used to calculate free energies at different temperatures (considered in G_mRRHO and δG_solv[only COSMO-RS]). The temperature range will only be evaluated if multitemp is set to on. |
multitemp |
Evaluate free energies at different temperatures defined in trange. |
evaluate_rrho |
Option to consider /not consider thermostatistical contributions. |
consider_sym |
Option to consider symmetry in the thermostatistical contribution (only xtb) |
bhess |
Calculate single point hessians (SPH) on the geometry, instead of “ohess” (optimization + hessian calculation) |
imagthr |
threshold for inverting imaginary frequencies for thermostatistical contributions (in cm-1 ). Internal defaults are applied if set to automatic. |
sthr |
rotor cut-off (in cm-1 ) used for the thermostatical contributions. Internal defaults are applied if set to automatic. |
scale |
scaling factor for frequencies in vibrational partition function. Internal defaults are applied if set to automatic. |
rmsdbias |
gESC related, using rmsdpot.xyz to be consistent to CREST. |
sm_rrho |
solvent model applied in the GFNn-xTB thermostatistical contribution calculation. |
check |
Terminate the CENSO run if too many calculations crash. |
prog |
QM code used for part0, part1 and part2, this can be TURBOMOLE or ORCA. |
func |
functional used in part1 (prescreening) and part2 (optimization) |
basis |
basis set used in combination with func in part1 (prescreening) and part2 (optimization). If basis is set to automatic the basis set is chosen internally. |
maxthreads |
Used for parallel calculation. Maxthreads determines the number of independent calculations running in parallel. E.g. resulting in 4 independent single-point /optimization calculations. |
omp |
Used for parallel calculation. Omp determines the number of cores each independent calculation can use. Eg. maxthreads = 4 and omp = 5 resulting in 4 independent calculations and each independent calculation uses 5 cores. |
cosmorsparam |
Flag for choosing COSMO-RS parameterizations. If set to automatic the input from the COSMO-RS input line is chosen. |
Part0 - Cheap-Prescreening - Settings¶
keyword |
definition |
|---|---|
part0 |
Option to turn the “cheap prescreening part” on or off. |
func0 |
Functional used in part0. |
basis0 |
Basis set used in combination with func0. If basis0 is set to automatic the basis set is chosen internally. |
part0_gfnv |
GFN version employed in the thermostatistical contribution in part0. |
part0_threshold |
Threshold/Energy-window (kcal/mol) within which all conformers are considered. |
Part1 - Prescreening - Settings¶
keyword |
definition |
|---|---|
part1 |
Option to turn the “prescreening part” on or off. |
smgsolv1 |
Additive solvation contribution employed in part1. |
part1_gfnv |
GFN version employed in the thermostatistical contribution in part1. |
part1_threshold |
Threshold/Energy-window (kcal/mol) within which all conformers are considered further. |
Part2 - Optimization - Settings¶
keyword |
definition |
|---|---|
part2 |
Option to turn the “optimization” part on or off. |
opt_limit |
Threshold/Energy-window (kcal/mol) within which all conformers are fully optimized. |
sm2 |
Implicit solvation model used in the optimization (for the implicit effect on the geometry). |
smgsolv2 |
Additive solvation model used for calculation of δG_solv in part2 (used to calculate contribution to free energy). |
part2_gfnv |
GFN version employed in the thermostatistical (G_mRRHO) contribution in part2. |
ancopt |
Using ANCoptimizer implemented in xTB for geometry optimization. |
hlow |
Lowest force constant in ANC generation, used with ancopt. |
opt_spearman |
Using the new ensemble-optimizer, employing batch-wise metacycles. |
part2_threshold |
Boltzmann threshold in % within which all conformers are considered further. E.g. 90 %; all conformers up to a sum of 90 % are considered. |
optlevel2 |
Optimization threshold in the geometry optimization. If set to automatic internal defaults will be used. |
optcycles |
Number of optimization iterations performed within one cycle in the ensemble optimizer. |
spearmanthr |
Spearman rank correlation coeff. used to determine if PES during geometry optimization can be assumed parallel. |
radsize |
Setting of the radial grid size for func used in part2. |
crestcheck |
Automatically sort out conformers which might have become identical or rotamers during DFT geometry optimization. Check is performed using CREST (this is threshold based, so use with care). |
Part3 - Refinement - Settings¶
keyword |
definition |
|---|---|
part3 |
Option to turn the “refinement” part on or off. |
prog3 |
QM code used for part3 this can be TURBOMOLE or ORCA. |
func3 |
functional used in part3 (refinement) |
basis3 |
basis set employed in combination with func3. If basis3 is set to automatic the basis set is chosen internally (mainly for composite methods). |
smgsolv3 |
Additive solvation model used for calculation of δG_solv in part3. |
part3_gfnv |
GFN version employed in the thermostatistical contribution in part3. |
part3_threshold |
Boltzmann threshold in % within which all conformers are considered further. E.g. 90 %, all conformers up to a sum of 90 % are considered. |
Part4 - NMR- Settings¶
keyword |
definition |
|---|---|
part4 |
Option to turn the “NMR property part” on or off. |
couplings |
Perform coupling constant calculations [options are on or off]. |
progJ |
QM code (TM, ORCA) used for coupling constant calculations. |
funcJ |
Density functional employed for the coupling constant calculation. |
basisJ |
basis set employed with the DFA (funcJ) for coupling constant calculations. |
sm4J |
implicit solvent model employed in the coupling constant calculation. |
shieldings |
Perform shielding constant calculations [options are on or off]. |
progS |
QM code (TM, ORCA) used for shielding constant calculations. |
funcS |
Density functional employed for the shielding constant calculation. |
basisS |
basis set employed with the DFA (funcS) for shielding constant calculations. |
sm4S |
implicit solvent model employed in the shielding constant calculation. |
reference_1H |
Reference molecule to convert 1H shielding constants to shifts e.g. TMS. |
reference_13C |
Reference molecule to convert 13C shielding constants to shifts e.g. TMS. |
reference_19F |
Reference molecule to convert 19F shielding constants to shifts e.g. CFCl3. |
reference_29Si |
Reference molecule to convert 29Si shielding constants to shifts e.g. TMS. |
reference_31P |
Reference molecule to convert 31P shielding constants to shifts e.g. TMP. |
1H_active |
Calculate 1H NMR properties [options are on or off]. |
13C_active |
Calculate 13C NMR properties [options are on or off]. |
19F_active |
Calculate 19F NMR properties [options are on or off]. |
29Si_active |
Calculate 29Si NMR properties [options are on or off]. |
31P_active |
Calculate 31P NMR properties [options are on or off]. |
resonance_frequency |
Resonance frequency of the experimental spectrometer (in Hz). |
Optical Rotation Property Settings¶
keyword |
definition |
|---|---|
optical_rotation |
Option to turn the “OR property part” on or off. |
funcOR |
Functional employed to calculate the optical rotatory (OR) dispersion. |
funcOR_SCF |
Functional to generate converged MOs. |
basisOR |
Basis set employed for the OR calculation. |
frequency_optical_rot |
List of frequencies in nm to evaluate OR at e.g. [589.0]. |
Thresholds¶
CENSO is a threshold based sorting algorithm. The thresholds have been determined for typical drug-like organic molecules up to 200 atoms. For cases with high flexibility or very different conformer ordering between SQM/FF and DFT it can be necessary to increase the thresholds. If your target quantity is an averaged ensemble free energy, be sure not to use small energy windows in part0 and part1, as this can falsely reduce the ensemble size.
In the following the employed thresholds are listed and their use is explained:
Part0 - Cheap Prescreening¶
- part0_threshold = g_thr(0)
- cml
-part0_threshold- censorc
part0_threshold
part0_threshold g_thr(0) is an energy window /threshold in kcal/mol within which all conformers are considered. The CENSO internal default for g_thr(0) = 4.0 kcal/mol. The sorting threshold is designed to remove conformers very high lying in electronic energy (E).
Part1 - Prescreening¶
In part1 two sorting steps are applied. One based on g_thr(1) with improved energy and solvation description and one on G_thr(1) where thermostatistical contributions have been calculated additionally.
- part1_threshold = g_thr(1) and G_thr(1)
- cml
-part1_threshold- censorc
part1_threshold
part1_threshold g_thr(1) is an energy window /threshold in kcal/mol within which all conformers are considered. The CENSO internal default for g_thr(1) = 3.5 kcal/mol. The sorting threshold g_thr(1) is designed to remove high lying conformers based on improved electronic energy (E) and solvation contributions (δG_solv). G_thr(1) sorting is based on full free energy including thermostatistical contributions (G_mRRHO). Both, g_thr(1) and G_thr(1) use the same base threshold e.g. 3.5 kcal/mol and G_thr(1) can be automatically increased as a function of the standard deviation of G_mRRHO in the structure ensemble, indicating high structural diversity and possibly larger errors (fuzzy sorting).
Part2 - Optimization¶
In part2 two sorting thresholds are applied. One which is applied during geometry optimization and one Boltzmann sum threshold.
- threshold applied during optimization G_thr(opt,2)
- cml
-opt_limit- censorc
opt_limit
- Spearman-threshold for testing for parallel PES
- cml
-spearmanthr- censorc
spearmanthr
- Boltzmann sum threshold G_thr(2)
- cml
-thrpart2- censorc
part2_threshold
The internal default for G_thr(opt,2) is set to 2.5 kcal/mol. During the geometry optimization the initial threshold G_thr(opt,2) is increased by 60 % (or at least 1.5 kcal/mol). If the PES can be assumed parallel (tested by a Spearman rank coefficient) the threshold is decresed until it reaches the initial value. All conformers with (free) energies above the G_thr(opt,2) threshold are discarded and all conformers below G_thr(opt,2) will by fully DFT optimized. The last threshold employed in part2 is a Boltzmann sum threshold G_thr(2) and all populated conformers of the ensemble, up to the Boltzmann population (in %) are considered further.
Part3 - Refinement¶
In part3 a Boltzmann sum threshold is employed.
- Boltzmann sum threshold G_thr(3):
- cml
-thrpart3- censorc
part3_threshold
Based on high level free energies Boltzmann weights are calculated and all conformers up to the Boltzmann sum threshold (in %) are considered further.
Part4 - NMR properties¶
In part4 only Boltzmann sum thresholds of part2 G_thr(2) or part3 G_thr(3) are applied. It is possible to calculate part4 using Boltzmann weights from part1, but since there is no Boltzmann sum threshold in part1, in this case, the threshold G_thr(2) is used. The NMR properties are calculated on populated conformers up to the Boltzmann threshold in %.
Part5 - Optical rotatory dispersion¶
In part4 only Boltzmann sum thresholds of part2 G_thr(2) or part3 G_thr(3) are applied. It is possible to calculate part5 using Boltzmann weights from part1, but since there is no Boltzmann sum threshold in part1, in this case, the threshold G_thr(2) is used. The OR property is calculated on populated conformers up to the Boltzmann threshold in %. For optical rotation it is necessary to include almost the entire ensemble e.g. 99 %
Solvation¶
CENSO uses several QM-packages and not all solvents are available for all solvation models throughout the QM-codes. For this reason a user editable file is created in the folder ~/.censo_assets:
$ ~/.censo_assets/censo_solvents.json
{
"acetone":{
"cosmors": ["propanone_c0", "propanone_c0"],
"dcosmors": ["propanone", "propanone"],
"xtb": ["acetone", "acetone"],
"cpcm": ["acetone", "acetone"],
"smd": ["ACETONE", "ACETONE"],
"DC": 20.7
},
"chcl3":{
"cosmors": ["chcl3_c0", "chcl3_c0"],
"dcosmors": ["chcl3", "chcl3"],
"xtb": ["chcl3", "chcl3"],
"cpcm": ["chloroform","chloroform"],
"smd": ["CHLOROFORM", "CHLOROFORM"],
"DC": 4.8
},
"acetonitrile":{
"cosmors": ["acetonitrile_c0", "acetonitrile_c0"],
"dcosmors": ["acetonitrile", "acetonitrile"],
"xtb": ["acetonitrile", "acetonitrile"],
"cpcm": ["acetonitrile", "acetonitrile"],
"smd": ["ACETONITRILE", "ACETONITRILE"],
"DC": 36.6
},
"ch2cl2":{
"cosmors": ["ch2cl2_c0", "ch2cl2_c0"],
"dcosmors": [null, "chcl3"],
"xtb": ["ch2cl2", "ch2cl2"],
"cpcm": ["CH2Cl2", "CH2Cl2"],
"smd": ["DICHLOROMETHANE", "DICHLOROMETHANE"],
"DC": 9.1
},
"dmso":{
"cosmors": ["dimethylsulfoxide_c0", "dimethylsulfoxide_c0"],
"dcosmors": ["dimethylsulfoxide", "dimethylsulfoxide"],
"xtb": ["dmso", "dmso"],
"cpcm": ["DMSO", "DMSO"],
"smd": ["DIMETHYLSULFOXIDE", "DIMETHYLSULFOXIDE"],
"DC": 47.2
},
"h2o":{
"cosmors": ["h2o_c0", "h2o_c0"],
"dcosmors": ["h2o", "h2o"],
"xtb": ["h2o", "h2o"],
"cpcm": ["Water", "Water"],
"smd": ["WATER", "WATER"],
"DC": 80.1
},
"methanol":{
"cosmors": ["methanol_c0", "methanol_c0"],
"dcosmors": ["methanol", "methanol"],
"xtb": ["methanol", "methanol"],
"cpcm": ["Methanol", "Methanol"],
"smd": ["METHANOL", "METHANOL"],
"DC": 32.7
},
"thf":{
"cosmors": ["thf_c0", "thf_c0"],
"dcosmors": ["thf", "thf"],
"xtb": ["thf", "thf"],
"cpcm": ["THF", "THF"],
"smd": ["TETRAHYDROFURAN", "TETRAHYDROFURAN"],
"DC": 7.6
},
"toluene":{
"cosmors": ["toluene_c0", "toluene_c0"],
"dcosmors": ["toluene", "toluene"],
"xtb": ["toluene", "toluene"],
"cpcm": ["Toluene", "Toluene"],
"smd": ["TOLUENE", "TOLUENE"],
"DC": 2.4
},
"octanol":{
"cosmors": ["1-octanol_c0", "1-octanol_c0"],
"dcosmors": ["octanol", "octanol"],
"xtb": ["octanol", "octanol"],
"cpcm": ["Octanol", "Octanol"],
"smd": ["1-OCTANOL", "1-OCTANOL"],
"DC": 9.9
},
"woctanol":{
"cosmors": [null, "woctanol"],
"dcosmors": ["wet-otcanol", "wet-octanol"],
"xtb": ["woctanol", "woctanol"],
"cpcm": [null, "Octanol"],
"smd": [null, "1-OCTANOL"],
"DC": 8.1
},
"hexadecane":{
"cosmors": ["n-hexadecane_c0", "n-hexadecane_c0"],
"dcosmors": ["hexadecane", "hexadecane"],
"xtb": ["hexadecane", "hexadecane"],
"cpcm": [null, "Hexane"],
"smd": ["N-HEXADECANE", "N-HEXADECANE"],
"DC": 2.1
},
"dmf":{
"cosmors": ["dimethylformamide_c0","dimethylformamide_c0"],
"dcosmors": [null, "dimethylsulfoxide"],
"xtb": ["dmf", "dmf"],
"cpcm": ["DMF", "DMF"],
"smd": ["N,N-DIMETHYLFORMAMIDE", "N,N-DIMETHYLFORMAMIDE"],
"DC": 38.3
},
"aniline":{
"cosmors": ["aniline_c0", "aniline_c0"],
"dcosmors": ["aniline", "aniline"],
"xtb": ["aniline", "aniline"],
"cpcm": [null,"Pyridine"],
"smd": ["ANILINE", "ANILINE"],
"DC": 6.9
},
"cyclohexane":{
"cosmors": ["cyclohexane_c0", "cyclohexane_c0"],
"dcosmors": ["cyclohexane", "cyclohexane"],
"xtb": [null, "hexane"],
"cpcm": ["Cyclohexane", "Cyclohexane"],
"smd": ["CYCLOHEXANE", "CYCLOHEXANE"],
"DC": 2.0
},
"ccl4":{
"cosmors": ["ccl4_c0", "ccl4_c0"],
"dcosmors": ["ccl4", "ccl4"],
"xtb": ["ccl4", "ccl4"],
"cpcm": ["CCl4", "CCl4"],
"smd": ["CARBON TETRACHLORIDE", "CARBON TETRACHLORIDE"],
"DC": 2.2
},
"diethylether":{
"cosmors": ["diethylether_c0", "diethylether_c0"],
"dcosmors": ["diethylether", "diethylether"],
"xtb": ["ether", "ether"],
"cpcm": [null, "THF"],
"smd": ["DIETHYL ETHER", "DIETHYL ETHER"],
"DC": 4.4
},
"ethanol":{
"cosmors": ["ethanol_c0", "ethanol_c0"],
"dcosmors": ["ethanol", "ethanol"],
"xtb": ["ethanol", "ethanol"],
"cpcm": [null, "Methanol"],
"smd": ["ETHANOL", "ETHANOL"],
"DC": 24.6
},
"hexane":{
"cosmors": ["hexane_c0", "hexane_c0"],
"dcosmors": ["hexane", "hexane"],
"xtb": ["hexane", "hexane"],
"cpcm": ["Hexane", "Hexane"],
"smd": ["N-HEXANE", "N-HEXANE"],
"DC": 1.9
},
"nitromethane":{
"cosmors": ["nitromethane_c0", "nitromethane_c0"],
"dcosmors": ["nitromethane", "nitromethane"],
"xtb": ["nitromethane", "nitromethane"],
"cpcm": [null, "methanol"],
"smd": "",
"DC": 38.2
},
"benzaldehyde":{
"cosmors": ["benzaldehyde_c0", "benzaldehyde_c0"],
"dcosmors": [null, "propanone"],
"xtb": ["benzaldehyde", "benzaldehyde"],
"cpcm": [null, "Pyridine"],
"smd": ["BENZALDEHYDE", "BENZALDEHYDE"],
"DC": 18.2
},
"benzene":{
"cosmors": ["benzene_c0", "benzene_c0"],
"dcosmors": [null, "toluene"],
"xtb": ["benzene", "benzene"],
"cpcm": ["Benzene", "Benzene"],
"smd": ["BENZENE", "BENZENE"],
"DC": 2.3
},
"cs2":{
"cosmors": ["cs2_c0", "cs2_c0"],
"dcosmors": [null, "ccl4"],
"xtb": ["cs2", "cs2"],
"cpcm": [null, "CCl4"],
"smd": ["CARBON DISULFIDE", "CARBON DISULFIDE"],
"DC": 2.6
},
"dioxane":{
"cosmors": ["dioxane_c0", "dioxane_c0"],
"dcosmors": [null, "diethylether"],
"xtb": ["dioxane", "dioxane"],
"cpcm": [null, "Cyclohexane"],
"smd": ["1,4-DIOXANE", "1,4-DIOXANE"],
"DC": 2.2
},
"ethylacetate":{
"cosmors": ["ethylacetate_c0", "ethylacetate_c0"],
"dcosmors": [null, "diethylether"],
"xtb": ["ethylacetate", "ethylacetate"],
"cpcm": [null, "THF"],
"smd": ["ETHYL ETHANOATE", "ETHYL ETHANOATE"],
"DC": 5.9
},
"furan":{
"cosmors": ["furane_c0", "furane_c0"],
"dcosmors": [null, "diethylether"],
"xtb": ["furane", "furane"],
"cpcm": [null, "THF"],
"smd": [null, "THF"],
"DC": 3.0
},
"phenol":{
"cosmors": ["phenol_c0", "phenol_c0"],
"dcosmors": [null, "thf"],
"xtb": ["phenol", "phenol"],
"cpcm": [null, "THF"],
"smd": [null, "THIOPHENOL"],
"DC": 8.0
}
}
The file contains a dictionary of all available solvent models and solvents. If a solvent is not available with a certain solvent model, the user can then choose a replacement solvent within the same solvation model. E.g. if benzene is not available in DCOSMO-RS choose toluene in DCOSMO-RS.
{ # EXAMPLE
"solvent-name-in-CENSO":{
"solvent-model1": ["solvent-name in solvent model","solvent-name USED in solvent model"],
"solvent-model2": ["null = solvent not found"," replacement solvent USED"],
"xtb represents ALPB or GBSA" : ["solvent", "solvent],
"DC = Dielectric Constant: Used for COSMO and DCOSMO-RS
},
# END EXAMPLE
"acetonitrile":{
"cosmors": ["acetonitrile_c0", "acetonitrile_c0"],
"dcosmors": ["acetonitrile", "acetonitrile"],
"xtb": ["acetonitrile", "acetonitrile"],
"cpcm": ["acetonitrile", "acetonitrile"],
"smd": ["ACETONITRILE", "ACETONITRILE"],
"DC": 36.6
},
"ch2cl2":{
"cosmors": ["ch2cl2_c0", "ch2cl2_c0"],
"dcosmors": [null, "chcl3"],
"xtb": ["ch2cl2", "ch2cl2"],
"cpcm": ["CH2Cl2", "CH2Cl2"],
"smd": ["DICHLOROMETHANE", "DICHLOROMETHANE"],
"DC": 9.1
},
}
Warning
The solvent file is directly used in censo and typos will cause the calculations to crash!
Adding a new solvent is as easy as adding a new dictionary entry to the file.
In CENSO several solvent models can be applied. The intention is either a good description of the free energy (keyword: smgsolv) or an implicit effect on a property or geometry (keyword: sm).
(sm) implicit solvation for properties:
COSMO [TM]
CPCM [ORCA]
DCOSMO-RS [TM]
ALPB [xtb]
GBSA [xtb]
SMD [ORCA]
(smgsolv) implicit solvation for free energies:
COSMO-RS [COSMO-RS]
SMD_Gsolv [ORCA]
ALPB_Gsolv [xtb]
GBSA_Gsolv [xtb]
Trouble shooting¶
CENSO is designed as an automated workflow. It can happen that for example single-point calculations fail. In this case CENSO will consider this calculation as failed and sort out the corresponding conformer/structure. The calculation is not retried but can be manually checked and the results can be written to enso.json. With the updated enso.json the calculation can be restarted.
If many or all single-point calculations fail, this is a very good indication that either:
the input geometry is far from being reasonable
maybe a missing charge information
a technical problem e.g., missing information on the QM program path
Usage examples¶
CENSO can be used for several applications / target quantities. Some are listed below:
Hint
CENSO has sorting “parts” which can be turned on and off. The parts are run in sequence and the sorting-results are influenced by the choice of sorting-parts employed. If for example the optimization part (part2) is not performed, then all subsequent parts will calculate free energies or properties on the input SQM/FF geometries (not DFT optimized geometries)! Each part contains thresholds (see Threshold) and choosing to low (free) energy windows (in the early sorting parts) will affect your final ensemble / averaged free energy / property.
Note
For the demonstration purpose it is assumed that all parts are turned off in the global configuration file of the user!
Calculate fast DFT(B97-D3(0)/def2-SV(P)+gcp) single-point energies on GFNn-xTB input geometries¶
Hint
Useful in case of large structure ensembles (SE). Very efficient (fast) improvement on the electronic energy description compared to the initial SQM/FF energies. High lying conformers are quickly sorted out.
$ censo -inp ensemble.xyz -part0 on -chrg 1 -solvent h2o > censo.out &
______________________________________________________________
| |
| |
| CENSO - Commandline ENSO |
| v 1.0.3 |
| energetic sorting of CREST Conformer Rotamer Ensembles |
| University of Bonn, MCTC |
| Feb 2021 |
| based on ENSO version 2.0.1 |
| F. Bohle and S. Grimme |
| |
|______________________________________________________________|
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
----------------------------------------------------------------------------------------------------
PARAMETERS
----------------------------------------------------------------------------------------------------
The configuration file .censorc is read from /home/bohle/1projects/from_tmp1/CENSO/documentation-calcs/1-part0/.censorc.
Reading conformer rotamer ensemble from: /home/bohle/1projects/from_tmp1/CENSO/documentation-calcs/1-part0/ensemble.xyz.
Reading file: censo_solvents.json
--------------------------------------------------
CRE SORTING SETTINGS
--------------------------------------------------
number of atoms in system: 25
number of considered conformers: 22
number of all conformers from input: 22
charge: 1
unpaired: 0
solvent: h2o
temperature: 298.15
evaluate at different temperatures: on
temperature range: 273.15, 278.15, 283.15, 288.15, ...
calculate mRRHO contribution: on
consider symmetry for mRRHO contribution: off
cautious checking for error and failed calculations: on
checking the DFT-ensemble using CREST: off
maxthreads: 2
omp: 2
--------------------------------------------------
CRE CHEAP-PRESCREENING - PART0
--------------------------------------------------
part0: on
starting number of considered conformers: 22
program for part0: tm
functional for fast single-point: b97-d
basis set for fast single-point: def2-SV(P)
threshold g_thr(0) for sorting in part0: 4.0
Solvent model used with xTB: alpb
short-notation:
b97-d-D3/def2-SV(P) // GFNn-xTB (Input geometry)
END of parameters
------------------------------------------------------------
PATHS of external QM programs
------------------------------------------------------------
The following program paths are used:
xTB: /home/abt-grimme/AK-bin/xtb
TURBOMOLE: /home/abt-grimme/TURBOMOLE.7.5.1/bin/em64t-unknown-linux-gnu_smp
Using cefine from /home/bohle/bin/cefine
PARNODES for TM or COSMO-RS calculation was set to 2
----------------------------------------------------------------------------------------------------
Processing data from previous run (enso.json)
----------------------------------------------------------------------------------------------------
INFORMATION: No restart information exists and is created during this run!
----------------------------------------------------------------------------------------------------
CRE CHEAP-PRESCREENING - PART0
----------------------------------------------------------------------------------------------------
program: tm
functional for part0: b97-d
basis set for part0: def2-SV(P)
threshold g_thr(0): 4.0
starting number of considered conformers: 22
Calculating efficient gas-phase single-point energies:
The efficient gas-phase single-point is calculated for:
CONF1, CONF2, CONF3, CONF4, CONF5, CONF6, CONF7, CONF8, CONF9, CONF10, CONF11
CONF12, CONF13, CONF14, CONF15, CONF16, CONF17, CONF18, CONF19, CONF20, CONF21, CONF22
Constructed folders!
Starting 22 ALPB-Gsolv calculations
Running single-point in CONF1/part0_sp
Running single-point in CONF2/part0_sp
Running ALPB_GSOLV calculation in 1-part0/CONF1/part0_sp
Running ALPB_GSOLV calculation in 1-part0/CONF2/part0_sp
Running single-point in CONF3/part0_sp
Running single-point in CONF4/part0_sp
Running ALPB_GSOLV calculation in 1-part0/CONF3/part0_sp
Running ALPB_GSOLV calculation in 1-part0/CONF4/part0_sp
Running single-point in CONF5/part0_sp
Running single-point in CONF6/part0_sp
Running ALPB_GSOLV calculation in 1-part0/CONF5/part0_sp
Running ALPB_GSOLV calculation in 1-part0/CONF6/part0_sp
Running single-point in CONF7/part0_sp
Running single-point in CONF8/part0_sp
Running ALPB_GSOLV calculation in 1-part0/CONF7/part0_sp
Running ALPB_GSOLV calculation in 1-part0/CONF8/part0_sp
Running single-point in CONF9/part0_sp
Running single-point in CONF10/part0_sp
Running ALPB_GSOLV calculation in 1-part0/CONF9/part0_sp
Running ALPB_GSOLV calculation in 1-part0/CONF10/part0_sp
Running single-point in CONF11/part0_sp
Running single-point in CONF12/part0_sp
Running ALPB_GSOLV calculation in 1-part0/CONF11/part0_sp
Running ALPB_GSOLV calculation in 1-part0/CONF12/part0_sp
Running single-point in CONF13/part0_sp
Running single-point in CONF14/part0_sp
Running ALPB_GSOLV calculation in 1-part0/CONF13/part0_sp
Running ALPB_GSOLV calculation in 1-part0/CONF14/part0_sp
Running single-point in CONF15/part0_sp
Running single-point in CONF16/part0_sp
Running ALPB_GSOLV calculation in 1-part0/CONF15/part0_sp
Running ALPB_GSOLV calculation in 1-part0/CONF16/part0_sp
Running single-point in CONF17/part0_sp
Running single-point in CONF18/part0_sp
Running ALPB_GSOLV calculation in 1-part0/CONF17/part0_sp
Running ALPB_GSOLV calculation in 1-part0/CONF18/part0_sp
Running single-point in CONF19/part0_sp
Running single-point in CONF20/part0_sp
Running ALPB_GSOLV calculation in 1-part0/CONF19/part0_sp
Running ALPB_GSOLV calculation in 1-part0/CONF20/part0_sp
Running single-point in CONF21/part0_sp
Running single-point in CONF22/part0_sp
Running ALPB_GSOLV calculation in 1-part0/CONF21/part0_sp
Running ALPB_GSOLV calculation in 1-part0/CONF22/part0_sp
Tasks completed!
The efficient gas-phase single-point was successful for CONF1/part0_sp: E(DFT) = -496.55110270 Gsolv = -0.12279245
The efficient gas-phase single-point was successful for CONF2/part0_sp: E(DFT) = -496.55473079 Gsolv = -0.12241044
The efficient gas-phase single-point was successful for CONF3/part0_sp: E(DFT) = -496.55551554 Gsolv = -0.12099969
The efficient gas-phase single-point was successful for CONF4/part0_sp: E(DFT) = -496.55384665 Gsolv = -0.12156811
The efficient gas-phase single-point was successful for CONF5/part0_sp: E(DFT) = -496.55341065 Gsolv = -0.12251050
The efficient gas-phase single-point was successful for CONF6/part0_sp: E(DFT) = -496.55368828 Gsolv = -0.12175678
The efficient gas-phase single-point was successful for CONF7/part0_sp: E(DFT) = -496.54759208 Gsolv = -0.12365913
The efficient gas-phase single-point was successful for CONF8/part0_sp: E(DFT) = -496.55118920 Gsolv = -0.12200372
The efficient gas-phase single-point was successful for CONF9/part0_sp: E(DFT) = -496.54970422 Gsolv = -0.12167549
The efficient gas-phase single-point was successful for CONF10/part0_sp: E(DFT) = -496.55157272 Gsolv = -0.12001541
The efficient gas-phase single-point was successful for CONF11/part0_sp: E(DFT) = -496.54991969 Gsolv = -0.12296934
The efficient gas-phase single-point was successful for CONF12/part0_sp: E(DFT) = -496.55212770 Gsolv = -0.11751864
The efficient gas-phase single-point was successful for CONF13/part0_sp: E(DFT) = -496.55077718 Gsolv = -0.11854291
The efficient gas-phase single-point was successful for CONF14/part0_sp: E(DFT) = -496.55028792 Gsolv = -0.12090071
The efficient gas-phase single-point was successful for CONF15/part0_sp: E(DFT) = -496.54987374 Gsolv = -0.12311773
The efficient gas-phase single-point was successful for CONF16/part0_sp: E(DFT) = -496.55360018 Gsolv = -0.11274054
The efficient gas-phase single-point was successful for CONF17/part0_sp: E(DFT) = -496.55289531 Gsolv = -0.11378052
The efficient gas-phase single-point was successful for CONF18/part0_sp: E(DFT) = -496.50423172 Gsolv = -0.16468285
The efficient gas-phase single-point was successful for CONF19/part0_sp: E(DFT) = -496.52384365 Gsolv = -0.14390846
The efficient gas-phase single-point was successful for CONF20/part0_sp: E(DFT) = -496.50481476 Gsolv = -0.16519450
The efficient gas-phase single-point was successful for CONF21/part0_sp: E(DFT) = -496.53860751 Gsolv = -0.13212346
The efficient gas-phase single-point was successful for CONF22/part0_sp: E(DFT) = -496.50938650 Gsolv = -0.15826546
----------------------------------------------------------------------------------------------------
Removing high lying conformers by improved energy description
----------------------------------------------------------------------------------------------------
CONF# G [Eh] ΔG [kcal/mol] E [Eh] Gsolv [Eh] Gtot ΔE(DFT) ΔGsolv ΔGtot
GFN2-xTB GFN2-xTB b97-d-D3(0)/def2-SV(P) alpb [Eh] [kcal/mol] [kcal/mol] [kcal/mol]
[ALPB] [ALPB] [gfn2]
CONF1 -34.1746819 0.00 -496.5511027 -0.1227924 -496.6738951 2.28 -0.24 2.04
CONF2 -34.1743917 0.18 -496.5547308 -0.1224104 -496.6771412 0.00 0.00 0.00 <------
CONF3 -34.1742792 0.25 -496.5555155 -0.1209997 -496.6765152 -0.49 0.89 0.39
CONF4 -34.1739821 0.44 -496.5538467 -0.1215681 -496.6754148 0.55 0.53 1.08
CONF5 -34.1740224 0.41 -496.5534106 -0.1225105 -496.6759212 0.83 -0.06 0.77
CONF6 -34.1736309 0.66 -496.5536883 -0.1217568 -496.6754451 0.65 0.41 1.06
CONF7 -34.1725555 1.33 -496.5475921 -0.1236591 -496.6712512 4.48 -0.78 3.70
CONF8 -34.1721876 1.57 -496.5511892 -0.1220037 -496.6731929 2.22 0.26 2.48
CONF9 -34.1719439 1.72 -496.5497042 -0.1216755 -496.6713797 3.15 0.46 3.62
CONF10 -34.1714765 2.01 -496.5515727 -0.1200154 -496.6715881 1.98 1.50 3.48
CONF11 -34.1712638 2.14 -496.5499197 -0.1229693 -496.6728890 3.02 -0.35 2.67
CONF12 -34.1704841 2.63 -496.5521277 -0.1175186 -496.6696463 1.63 3.07 4.70
CONF13 -34.1703687 2.71 -496.5507772 -0.1185429 -496.6693201 2.48 2.43 4.91
CONF14 -34.1694191 3.30 -496.5502879 -0.1209007 -496.6711886 2.79 0.95 3.74
CONF15 -34.1691431 3.48 -496.5498737 -0.1231177 -496.6729915 3.05 -0.44 2.60
CONF16 -34.1664418 5.17 -496.5536002 -0.1127405 -496.6663407 0.71 6.07 6.78
CONF17 -34.1661652 5.34 -496.5528953 -0.1137805 -496.6666758 1.15 5.42 6.57
CONF18 -34.1660003 5.45 -496.5042317 -0.1646828 -496.6689146 31.69 -26.53 5.16
CONF19 -34.1664801 5.15 -496.5238437 -0.1439085 -496.6677521 19.38 -13.49 5.89
CONF20 -34.1658387 5.55 -496.5048148 -0.1651945 -496.6700093 31.32 -26.85 4.48
CONF21 -34.1670164 4.81 -496.5386075 -0.1321235 -496.6707310 10.12 -6.10 4.02
CONF22 -34.1656180 5.69 -496.5093865 -0.1582655 -496.6676520 28.45 -22.50 5.95
----------------------------------------------------------------------------------------------------
--------------------------------------------------
Conformers considered further
--------------------------------------------------
These conformers are below the 4.000 kcal/mol g_thr(0) threshold.
CONF1, CONF2, CONF3, CONF4, CONF5, CONF6, CONF7, CONF8, CONF9, CONF10, CONF11
CONF14, CONF15
Calculating Boltzmann averaged (free) energy of ensemble on input geometries (not DFT optimized)!
temperature /K: avE(T) /a.u. avG(T) /a.u.
----------------------------------------------------------------------------------------------------
298.15 -496.5544580 -496.6764445 <<==part0==
----------------------------------------------------------------------------------------------------
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>END of Part0<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
Ran part0 in 32.8727 seconds
Part : #conf time
--------------------------------------------------
Input : 22 -
Part0_all : 13 32.87s
--------------------------------------------------
All parts : 32.87s
CENSO all done!
$CENSO global configuration file: .censorc
$VERSION:1.0.3
ORCA: /home/USER/orca_4_2_1_linux_x86-64_openmpi216
ORCA version: 4.2.1
GFN-xTB: xtb
CREST: crest
mpshift: mpshift
escf: escf
#COSMO-RS
ctd = BP_TZVPD_FINE_C30_1601.ctd cdir = "/home/USER/COSMOlogic/COSMOthermX19/COSMOtherm/CTDATA-FILES" ldir = "/home/USER/COSMOlogic/COSMOthermX19/COSMOtherm/CTDATA-FILES"
cosmothermversion: 19
$ENDPROGRAMS
$CRE SORTING SETTINGS:
$GENERAL SETTINGS:
nconf: all # ['all', 'number e.g. 10 up to all conformers']
charge: 0 # ['number e.g. 0']
unpaired: 0 # ['number e.g. 0']
solvent: gas # ['gas', 'acetone', 'chcl3', 'acetonitrile', 'ch2cl2', 'dmso', 'h2o', 'methanol', 'thf', '...']
prog_rrho: xtb # ['xtb', 'prog']
temperature: 298.15 # ['temperature in K e.g. 298.15']
trange: [273.15, 378.15, 5] # ['temperature range [start, end, step]']
multitemp: on # ['on', 'off']
evaluate_rrho: on # ['on', 'off']
consider_sym: off # ['on', 'off']
bhess: on # ['on', 'off']
imagthr: automatic # ['automatic or e.g., -100 # in cm-1']
sthr: automatic # ['automatic or e.g., 50 # in cm-1']
scale: automatic # ['automatic or e.g., 1.0 ']
rmsdbias: off # ['on', 'off']
sm_rrho: alpb # ['alpb', 'gbsa']
check: on # ['on', 'off']
prog: tm # ['tm', 'orca']
func: r2scan-3c # ['pbe', 'b97-d', 'pbeh-3c', 'tpss', 'b97-d3', 'r2scan-3c', 'b97-3c']
basis: automatic # ['automatic', 'def2-mSVP', 'def2-mTZVP', 'def2-mTZVP', 'def2-TZVP', '...']
maxthreads: 2 # ['number of threads e.g. 2']
omp: 2 # ['number cores per thread e.g. 4']
cosmorsparam: automatic # ['automatic', '12-fine', '12-normal', '13-fine', '13-normal', '14-fine', '...']
$PART0 - CHEAP-PRESCREENING - SETTINGS:
part0: off # ['on', 'off']
func0: b97-d # ['pbeh-3c', 'b97-3c', 'b97-d3', 'pbe', 'r2scan-3c', 'tpss', 'b97-d']
basis0: def2-SV(P) # ['automatic', 'def2-mSVP', 'def2-mTZVP', 'def2-mTZVP', 'def2-TZVP', '...']
part0_gfnv: gfn2 # ['gfn1', 'gfn2', 'gfnff']
part0_threshold: 4.0 # ['number e.g. 4.0']
$PART1 - PRESCREENING - SETTINGS:
# func and basis is set under GENERAL SETTINGS
part1: off # ['on', 'off']
smgsolv1: cosmors # ['alpb_gsolv', 'dcosmors', 'cosmo', 'smd', 'cosmors-fine', 'cpcm', 'gbsa_gsolv', '...']
part1_gfnv: gfn2 # ['gfn1', 'gfn2', 'gfnff']
part1_threshold: 3.5 # ['number e.g. 5.0']
$PART2 - OPTIMIZATION - SETTINGS:
# func and basis is set under GENERAL SETTINGS
part2: off # ['on', 'off']
opt_limit: 2.5 # ['number e.g. 4.0']
sm2: dcosmors # ['cosmo', 'cpcm', 'default', 'smd', 'dcosmors']
smgsolv2: cosmors # ['cosmors-fine', 'gbsa_gsolv', 'cosmo', 'cpcm', 'smd_gsolv', 'alpb_gsolv', 'smd', '...']
part2_gfnv: gfn2 # ['gfn1', 'gfn2', 'gfnff']
ancopt: on # ['on']
hlow: 0.01 # ['lowest force constant in ANC generation, e.g. 0.01']
opt_spearman: on # ['on', 'off']
part2_threshold: 99 # ['Boltzmann sum threshold in %. e.g. 95 (between 1 and 100)']
optlevel2: automatic # ['crude', 'sloppy', 'loose', 'lax', 'normal', 'tight', 'vtight', 'extreme', '...']
optcycles: 8 # ['number e.g. 5 or 10']
spearmanthr: -4.0 # ['value between -1 and 1, if outside set automatically']
radsize: 10 # ['number e.g. 8 or 10']
crestcheck: off # ['on', 'off']
$PART3 - REFINEMENT - SETTINGS:
part3: off # ['on', 'off']
prog3: prog # ['tm', 'orca', 'prog']
func3: pw6b95 # ['dsd-blyp', 'pw6b95', 'b97-d3', 'r2scan-3c', 'pbe0', 'wb97x']
basis3: def2-TZVPD # ['SVP', 'SV(P)', 'TZVP', 'TZVPP', 'QZVP', 'QZVPP', 'def2-SV(P)', 'def2-mSVP', '...']
smgsolv3: cosmors # ['alpb_gsolv', 'dcosmors', 'cosmo', 'smd', 'cosmors-fine', 'cpcm', 'gbsa_gsolv', '...']
part3_gfnv: gfn2 # ['gfn1', 'gfn2', 'gfnff']
part3_threshold: 99 # ['Boltzmann sum threshold in %. e.g. 95 (between 1 and 100)']
$NMR PROPERTY SETTINGS:
$PART4 SETTINGS:
part4: off # ['on', 'off']
couplings: on # ['on', 'off']
progJ: prog # ['tm', 'orca', 'adf', 'prog']
funcJ: pbe0 # ['tpss', 'pbe0', 'pbeh-3c']
basisJ: def2-TZVP # ['SVP', 'SV(P)', 'TZVP', 'TZVPP', 'QZVP', 'QZVPP', 'def2-SV(P)', 'def2-mSVP', '...']
sm4J: default # ['dcosmors', 'smd', 'cosmo', 'cpcm']
shieldings: on # ['on', 'off']
progS: prog # ['tm', 'orca', 'adf', 'prog']
funcS: pbe0 # ['dsd-blyp', 'pbeh-3c', 'tpss', 'pbe0', 'kt2']
basisS: def2-TZVP # ['SVP', 'SV(P)', 'TZVP', 'TZVPP', 'QZVP', 'QZVPP', 'def2-SV(P)', 'def2-mSVP', '...']
sm4S: default # ['dcosmors', 'smd', 'cosmo', 'cpcm']
reference_1H: TMS # ['TMS']
reference_13C: TMS # ['TMS']
reference_19F: CFCl3 # ['CFCl3']
reference_29Si: TMS # ['TMS']
reference_31P: TMP # ['TMP', 'PH3']
1H_active: on # ['on', 'off']
13C_active: on # ['on', 'off']
19F_active: off # ['on', 'off']
29Si_active: off # ['on', 'off']
31P_active: off # ['on', 'off']
resonance_frequency: 300.0 # ['MHz number of your experimental spectrometer setup']
$OPTICAL ROTATION PROPERTY SETTINGS:
$PART5 SETTINGS:
optical_rotation: off # ['on', 'off']
funcOR: pbe # ['functional for opt_rot e.g. pbe']
funcOR_SCF: r2scan-3c # ['functional for SCF in opt_rot e.g. r2scan-3c']
basisOR: def2-SVPD # ['basis set for opt_rot e.g. def2-SVPD']
frequency_optical_rot: [589.0] # ['list of freq in nm to evaluate opt rot at e.g. [589, 700]']
$END CENSORC
25
-34.15995484
O -2.7404108553 -0.9210263756 0.0505546155
O -0.6532148483 -1.7303331963 0.1381884568
N -2.1811530948 1.4662136641 -0.3280604715
N 1.9999042791 -1.6115147219 -0.1737452561
C 1.2832974514 1.7494376339 0.2478643443
C 0.0382242755 1.0547713107 0.8044626435
C 2.1972182535 0.8461961224 -0.5852172042
C -0.9624505804 0.6276788621 -0.2713633850
C 2.7304045776 -0.3664138808 0.1827513585
C -1.5037598584 -0.8390454546 0.0048901917
H 1.8561477225 2.1402514306 1.0892838382
H 0.9852377848 2.6009114549 -0.3642611073
H -0.4518270956 1.7282098745 1.5089809935
H 0.3322545004 0.1775252924 1.3825123935
H 1.6820235078 0.5059218506 -1.4832357051
H 3.0380251642 1.4546200515 -0.9165284484
H -0.4868586610 0.6089411942 -1.2530945560
H 2.6388482788 -0.2021893439 1.2562535001
H 3.7853986884 -0.5188774904 -0.0473087348
H -2.2380899515 2.1426216511 0.4407329422
H -2.3218532286 1.9466721688 -1.2205963738
H 2.3394829642 -2.3992859458 0.3882351555
H 0.9350292280 -1.5547588441 -0.0165809300
H 2.1475890354 -1.8368760327 -1.1636223077
H -2.9328940343 0.6971914121 -0.1921053926
25
-34.15944839
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H -1.7780292676 0.5566802205 1.3629478428
H 0.5935972201 -1.3552723672 1.1310943683
H 1.8230458958 -2.4842696303 0.9418471118
H 2.1352867113 -1.1124232113 1.8467861942
H -1.6994055067 2.2241075607 0.9291898687
25
-34.15141381
O -1.3943785432 -1.0307567325 0.9025777408
O -0.4225106153 -1.2766835982 -1.0942963862
N -2.1382332497 1.3072100696 0.6820859684
N 1.8303685962 -1.9710495392 0.0707587666
C 0.9607624662 1.6168605590 0.1707894371
C -0.1959862014 1.7114505222 -0.8393306352
C 1.9799050629 0.5013843169 -0.1348429740
C -1.4247901716 0.8500833461 -0.5368218294
C 1.9371661639 -0.6960029627 0.8273160062
C -1.0467465663 -0.6453837331 -0.2300826075
H 0.5821582777 1.4936196592 1.1855414824
H 1.4853467761 2.5717069600 0.1437592453
H 0.1684852019 1.4328271659 -1.8279890567
H -0.5295558410 2.7487716363 -0.9068101296
H 1.7990108513 0.1423863706 -1.1479579769
H 2.9805578856 0.9303497506 -0.1217137710
H -2.0885910031 0.8601550715 -1.4024758281
H 1.0694995988 -0.6377417602 1.4853144468
H 2.8334350246 -0.7245407799 1.4470296049
H -1.6564311817 2.0816802979 1.1506799283
H -3.1156981590 1.5603768219 0.5197984898
H 2.6238854975 -2.0888513426 -0.5678832194
H 1.7803639034 -2.7755595157 0.7040003308
H 0.9218328585 -1.9204346441 -0.4990801476
H -2.0745975566 0.3957317695 1.2728068192
25
-34.15122546
O -1.4776298354 -0.9779162840 0.9689911790
O -0.4925234496 -1.3628551244 -1.0036507954
N -2.1639329473 1.3683833598 0.5828976748
N 1.8796097534 -1.9018199765 -0.0324662357
C 0.9212842989 1.5787487906 0.2022882964
C -0.1575522111 1.5949891498 -0.8983466380
C 2.0807266384 0.5903317386 -0.0312863938
C -1.4336452672 0.8124987799 -0.5833640723
C 2.0372506913 -0.6914975753 0.8153963432
C -1.1077721831 -0.6712596326 -0.1784565029
H 0.4772061571 1.3762504059 1.1769048440
H 1.3491352329 2.5796760629 0.2516191005
H 0.2519128515 1.1866703660 -1.8221067218
H -0.4443786804 2.6264492546 -1.1098247151
H 2.1069094344 0.3214704229 -1.0870338715
H 3.0133169149 1.1098047495 0.1839278312
H -2.0690635873 0.7917157945 -1.4696202320
H 1.1994207751 -0.6693189818 1.5132782369
H 2.9569334194 -0.7921592267 1.3922309558
H -1.6800036187 2.1679532791 1.0053931771
H -3.1334683512 1.6233161070 0.3791665015
H 2.6232513605 -1.9579134554 -0.7362257317
H 1.8912989959 -2.7525757838 0.5392212719
H 0.9273933706 -1.8444066710 -0.5257136187
H -2.1333692549 0.5050567581 1.2388793063
25
-34.15102491
O -2.7007099152 -1.6852260154 -0.4665848832
O -3.5578446821 0.0350414384 0.6950996250
N -1.7249631955 1.6316108345 0.4298941943
N 4.8503432460 -0.2765578553 0.0049566510
C 1.1047501969 0.4501828237 -0.3379055216
C -0.1445140391 -0.2886936630 0.1459845288
C 2.3741940866 -0.2828979224 0.0965187068
C -1.4339016427 0.3793165613 -0.3028003047
C 3.6160850376 0.4539254738 -0.3951671902
C -2.6934727541 -0.5488189533 -0.0039847520
H 1.1202182595 1.4641232269 0.0631636060
H 1.0744507790 0.5160807326 -1.4261342120
H -0.1466884742 -0.3764861277 1.2347858649
H -0.1614173698 -1.3033571375 -0.2567289346
H 2.3826839006 -0.3550960319 1.1849100754
H 2.3458274825 -1.2937888279 -0.3120785959
H -1.4193517541 0.5529473168 -1.3796978179
H 3.6476836700 1.4575725004 0.0303995802
H 3.5908364898 0.5356651831 -1.4823627548
H -1.7888195298 2.4639789876 -0.1581990321
H -2.7206446817 1.3385249836 0.8116492773
H 5.6915565940 0.2174183391 -0.3259194480
H 4.8962264202 -0.3605243899 1.0314916029
H 4.8443782262 -1.2261178281 -0.3963638456
H -1.0847775954 1.7904079765 1.2125175138
25
-34.15096274
O -3.0664396656 -0.6811514259 0.4732552569
O -1.1830540829 -1.6357953168 -0.2743493731
N -2.5677177347 1.6455787239 -0.0357930901
N 3.4161836207 -1.4947231742 0.0043983586
C 1.0526738400 0.4198619079 -0.3271341828
C -0.1392962419 1.1756334823 0.2601668795
C 2.3301787116 0.6870764296 0.4694516416
C -1.4374925629 0.7826136622 -0.4432938226
C 3.5433351448 -0.0155439223 -0.1263696890
C -1.9232732343 -0.6849210780 -0.0466890927
H 1.1914397265 0.7321338619 -1.3635085567
H 0.7858921189 -0.6373779302 -0.3204311762
H 0.0218209785 2.2505182304 0.1468292069
H -0.2266241551 0.9455046686 1.3247226359
H 2.5278796928 1.7590277621 0.4727119199
H 2.1882724928 0.3782271446 1.5058219746
H -1.3025118280 0.8032883597 -1.5259809861
H 4.4479425383 0.3027435209 0.3921583620
H 3.6346463266 0.2349775607 -1.1836334244
H -3.0211573542 2.1410074345 -0.8045922540
H -3.2218629847 0.8371482423 0.3587042034
H 4.2253281871 -1.9726822174 -0.4155872948
H 3.3489651634 -1.7581308116 0.9983748528
H 2.5570336567 -1.8144640232 -0.4679619280
H -2.3203269015 2.3008181314 0.7098687755
25
-34.15085064
O -3.5353488917 0.0322108098 0.4084906022
O -2.4254579214 -1.9084093375 0.6284254091
N -1.7744403653 1.3652775888 -0.6438663864
N 4.1843308757 -0.1227935311 -1.0149931633
C 1.2054477125 0.3338345853 -0.2573250215
C -0.0723683835 -0.0922253390 0.4701395235
C 2.4067626747 0.2476116899 0.6871054133
C -1.3095998224 -0.0201188789 -0.4106994862
C 3.6989393857 0.7735207317 0.0732627710
C -2.5481677099 -0.7347193516 0.2919952398
H 1.1039179513 1.3593179418 -0.6150772671
H 1.3305507433 -0.3269971917 -1.1156830038
H -0.2323641779 0.5179203592 1.3619095074
H 0.0148258366 -1.1272987239 0.8068454593
H 2.1939049448 0.8432977651 1.5748900270
H 2.5356727482 -0.7824695024 1.0211816116
H -1.1430786561 -0.5391980852 -1.3555500184
H 4.4681954117 0.8303339300 0.8434799998
H 3.5410323285 1.7707403176 -0.3387001734
H -2.7959421798 1.2370421526 -0.2418926774
H -1.2663143192 2.0543977636 -0.0827359543
H 4.3101055621 -1.0795234870 -0.6518667702
H 3.4997443822 -0.1538144186 -1.7841531054
H 5.0842467659 0.2120203831 -1.3873716549
H -1.8037773550 1.6476905491 -1.6249441216
25
-34.15048917
O -1.9774584219 -0.8822136242 -1.3447844876
O -0.7353222350 -1.3040874260 0.4712779300
N -1.2018711229 0.8204001109 1.6759883927
N 1.9464051556 -1.6923491374 0.3496868798
C 0.8058411616 1.0462579377 -0.9468506072
C -0.4754178942 1.7785998054 -0.5275051890
C 1.8226970853 0.7789686777 0.1752315710
C -1.5019161161 0.9155320919 0.2220611780
C 2.6576744598 -0.4659344426 -0.1177787426
C -1.4255171488 -0.5796126398 -0.2987743324
H 1.2927227489 1.6467822241 -1.7161034319
H 0.5115436171 0.1136959367 -1.4299162738
H -0.9626535770 2.1244807715 -1.4395462399
H -0.2313854006 2.6631384020 0.0636669169
H 2.4836824282 1.6401220787 0.2631946203
H 1.3379895832 0.6415415675 1.1385387246
H -2.5044279955 1.3042479639 0.0511624497
H 3.6220420553 -0.4105315490 0.3870533340
H 2.8346807725 -0.5412209492 -1.1903941633
H -0.5537202797 1.5469435382 2.0029686770
H -2.0510266978 0.8448716653 2.2497725116
H 0.8939724574 -1.6086997720 0.2334441992
H 2.2630899289 -2.5235198565 -0.1606712473
H 2.1155048181 -1.8450780227 1.3513380594
H -0.7798223195 -0.1709536166 1.7101046448
25
-34.15043307
O -3.3078583007 -0.3518099727 0.5480566241
O -1.8441149941 -2.0073969491 0.1397595703
N -1.9672328473 1.5403727742 -0.2372000800
N 3.6044925126 -0.8358440764 -0.6659647320
C 1.1684565146 1.0446332415 -0.4943940738
C 0.1082467096 0.2177955398 0.2395309885
C 2.4785715426 1.1657908669 0.2896724500
C -1.2458520269 0.2676289576 -0.4513144135
C 3.1696429470 -0.1592315605 0.5890169973
C -2.2263428078 -0.8414226742 0.1422529421
H 0.7932826990 2.0569151989 -0.6482792542
H 1.3354698371 0.6191303209 -1.4843783659
H -0.0031461344 0.5661490514 1.2686433794
H 0.3791631733 -0.8378892566 0.2841197320
H 3.1579098277 1.8188328559 -0.2597110183
H 2.2713923792 1.6478155935 1.2450536588
H -1.1432114953 0.0569418065 -1.5170262136
H 2.5004236326 -0.8240708177 1.1341470919
H 4.0493855213 0.0280822082 1.2049984895
H -1.5070190112 2.1488324010 0.4454597884
H -2.1837208522 2.0584218679 -1.0901715209
H 4.2094106392 -0.2068158824 -1.2153183037
H 4.1256865653 -1.6973771969 -0.4514692989
H 2.7834959501 -1.0854874671 -1.2358687369
H -2.8845837684 1.1083956166 0.2016053653
Calculate free energies in solution phase (CHCl3) on GFNn-xTB geometries¶
Note
There are two options available:
Using part1 (prescreening) or
only using part3 and do not calculate part2 (optimization)
The difference between the two approaches is that Part3 applies tighter thresholds in the SCF.
$ censo -inp ensemble.xyz -part1 on -chrg 1 -solvent chcl3 -smgsolv1 cosmors -func r2scan-3c -basis automatic -P 4 -O 2 > censo.out &
______________________________________________________________
| |
| |
| CENSO - Commandline ENSO |
| v 1.0.3 |
| energetic sorting of CREST Conformer Rotamer Ensembles |
| University of Bonn, MCTC |
| Feb 2021 |
| based on ENSO version 2.0.1 |
| F. Bohle and S. Grimme |
| |
|______________________________________________________________|
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
----------------------------------------------------------------------------------------------------
PARAMETERS
----------------------------------------------------------------------------------------------------
The configuration file .censorc is read from /home/bohle/1projects/from_tmp1/CENSO/documentation-calcs/2-part1/.censorc.
Reading conformer rotamer ensemble from: /home/bohle/1projects/from_tmp1/CENSO/documentation-calcs/2-part1/ensemble.xyz.
Reading file: censo_solvents.json
--------------------------------------------------
CRE SORTING SETTINGS
--------------------------------------------------
number of atoms in system: 25
number of considered conformers: 22
number of all conformers from input: 22
charge: 1
unpaired: 0
solvent: chcl3
temperature: 298.15
evaluate at different temperatures: on
temperature range: 273.15, 278.15, 283.15, 288.15, ...
calculate mRRHO contribution: on
consider symmetry for mRRHO contribution: off
cautious checking for error and failed calculations: on
checking the DFT-ensemble using CREST: off
maxthreads: 4
omp: 2
--------------------------------------------------
CRE PRESCREENING - PART1
--------------------------------------------------
part1: on
starting number of considered conformers: 22
program for part1: tm
functional for initial evaluation: r2scan-3c
basis set for initial evaluation: def2-mTZVPP
calculate mRRHO contribution: on
program for mRRHO contribution: xtb
GFN version for mRRHO and/or GBSA_Gsolv: gfn2
Apply constraint to input geometry during mRRHO calculation: on
solvent model applied with xTB: alpb
evaluate at different temperatures: off
threshold g_thr(1) and G_thr(1) for sorting in part1: 3.5
solvent model for Gsolv contribution of part1: cosmors
short-notation:
r2scan-3c + COSMORS[chcl3] + GmRRHO(GFN2[alpb]-bhess) // GFNn-xTB (Input geometry)
END of parameters
------------------------------------------------------------
PATHS of external QM programs
------------------------------------------------------------
The following program paths are used:
xTB: /home/abt-grimme/AK-bin/xtb
TURBOMOLE: /home/abt-grimme/TURBOMOLE.7.5.1/bin/em64t-unknown-linux-gnu_smp
Setup of COSMO-RS:
ctd = BP_TZVPD_FINE_C30_1601.ctd
cdir = "/home/bohle/COSMOlogic/COSMOthermX19/COSMOtherm/CTDATA-FILES"
ldir = "/home/bohle/COSMOlogic/COSMOthermX19/COSMOtherm/CTDATA-FILES"
Using /home/bohle/COSMOlogic/COSMOthermX19/COSMOtherm/DATABASE-COSMO/BP-TZVP-COSMO
as path to the COSMO-RS NORMAL DATABASE.
Using cefine from /home/bohle/bin/cefine
PARNODES for TM or COSMO-RS calculation was set to 2
Using COSMOtherm from /home/bohle/COSMOlogic/COSMOthermX19/COSMOtherm/BIN-LINUX/cosmotherm
----------------------------------------------------------------------------------------------------
Processing data from previous run (enso.json)
----------------------------------------------------------------------------------------------------
INFORMATION: No restart information exists and is created during this run!
----------------------------------------------------------------------------------------------------
CRE PRESCREENING - PART1
----------------------------------------------------------------------------------------------------
program: tm
functional for part1 and 2: r2scan-3c
basis set for part1 and 2: def2-mTZVPP
Solvent: chcl3
solvent model for Gsolv contribution: cosmors
threshold g_thr(1) and G_thr(1): 3.5
starting number of considered conformers: 22
calculate mRRHO contribution: on
program for mRRHO contribution: xtb
GFN version for mRRHO and/or GBSA_Gsolv: gfn2
Apply constraint to input geometry during mRRHO calculation: on
temperature: 298.15
Calculating single-point energies and solvation contribution (G_solv):
The prescreening COSMO-RS is calculated for:
CONF1, CONF2, CONF3, CONF4, CONF5, CONF6, CONF7, CONF8, CONF9, CONF10, CONF11
CONF12, CONF13, CONF14, CONF15, CONF16, CONF17, CONF18, CONF19, CONF20, CONF21, CONF22
Constructed folders!
Constructed folders!
Starting 22 COSMO-RS-Gsolv calculations.
Running COSMO-RS calculation in CONF1/r2scan-3c/COSMO
Running COSMO-RS calculation in CONF2/r2scan-3c/COSMO
Running COSMO-RS calculation in CONF3/r2scan-3c/COSMO
Running COSMO-RS calculation in CONF4/r2scan-3c/COSMO
Running COSMO-RS calculation in CONF5/r2scan-3c/COSMO
Running COSMO-RS calculation in CONF6/r2scan-3c/COSMO
Running COSMO-RS calculation in CONF7/r2scan-3c/COSMO
Running COSMO-RS calculation in CONF8/r2scan-3c/COSMO
Running COSMO-RS calculation in CONF9/r2scan-3c/COSMO
Running COSMO-RS calculation in CONF10/r2scan-3c/COSMO
Running COSMO-RS calculation in CONF11/r2scan-3c/COSMO
Running COSMO-RS calculation in CONF12/r2scan-3c/COSMO
Running COSMO-RS calculation in CONF13/r2scan-3c/COSMO
Running COSMO-RS calculation in CONF14/r2scan-3c/COSMO
Running COSMO-RS calculation in CONF15/r2scan-3c/COSMO
Running COSMO-RS calculation in CONF16/r2scan-3c/COSMO
Running COSMO-RS calculation in CONF17/r2scan-3c/COSMO
Running COSMO-RS calculation in CONF18/r2scan-3c/COSMO
Running COSMO-RS calculation in CONF19/r2scan-3c/COSMO
Running COSMO-RS calculation in CONF20/r2scan-3c/COSMO
Running COSMO-RS calculation in CONF21/r2scan-3c/COSMO
Running COSMO-RS calculation in CONF22/r2scan-3c/COSMO
Tasks completed!
prescreening COSMO-RS calculation was successful for CONF1/r2scan-3c/COSMO: -0.09391084
prescreening COSMO-RS calculation was successful for CONF2/r2scan-3c/COSMO: -0.09344716
prescreening COSMO-RS calculation was successful for CONF3/r2scan-3c/COSMO: -0.09189166
prescreening COSMO-RS calculation was successful for CONF4/r2scan-3c/COSMO: -0.09269361
prescreening COSMO-RS calculation was successful for CONF5/r2scan-3c/COSMO: -0.09328873
prescreening COSMO-RS calculation was successful for CONF6/r2scan-3c/COSMO: -0.09278491
prescreening COSMO-RS calculation was successful for CONF7/r2scan-3c/COSMO: -0.09457155
prescreening COSMO-RS calculation was successful for CONF8/r2scan-3c/COSMO: -0.09275254
prescreening COSMO-RS calculation was successful for CONF9/r2scan-3c/COSMO: -0.09316162
prescreening COSMO-RS calculation was successful for CONF10/r2scan-3c/COSMO: -0.09116989
prescreening COSMO-RS calculation was successful for CONF11/r2scan-3c/COSMO: -0.09348580
prescreening COSMO-RS calculation was successful for CONF12/r2scan-3c/COSMO: -0.08900263
prescreening COSMO-RS calculation was successful for CONF13/r2scan-3c/COSMO: -0.08998048
prescreening COSMO-RS calculation was successful for CONF14/r2scan-3c/COSMO: -0.09122770
prescreening COSMO-RS calculation was successful for CONF15/r2scan-3c/COSMO: -0.09272288
prescreening COSMO-RS calculation was successful for CONF16/r2scan-3c/COSMO: -0.08509833
prescreening COSMO-RS calculation was successful for CONF17/r2scan-3c/COSMO: -0.08598277
prescreening COSMO-RS calculation was successful for CONF18/r2scan-3c/COSMO: -0.13224220
prescreening COSMO-RS calculation was successful for CONF19/r2scan-3c/COSMO: -0.11057302
prescreening COSMO-RS calculation was successful for CONF20/r2scan-3c/COSMO: -0.13223689
prescreening COSMO-RS calculation was successful for CONF21/r2scan-3c/COSMO: -0.09915029
prescreening COSMO-RS calculation was successful for CONF22/r2scan-3c/COSMO: -0.12536341
--------------------------------------------------
Removing high lying conformers
--------------------------------------------------
CONF# E(GFNn-xTB) ΔE(GFNn-xTB) E [Eh] Gsolv [Eh] Gtot ΔGtot
[a.u.] [kcal/mol] r2scan-3c COSMO-RS-normal [Eh] [kcal/mol]
[r2scan-3c]
CONF1 -34.1599548 0.00 -497.3021467 -0.0939108 -497.3960575 1.82
CONF2 -34.1594484 0.32 -497.3049956 -0.0934472 -497.3984428 0.33
CONF3 -34.1592530 0.44 -497.3064930 -0.0918917 -497.3983847 0.36
CONF4 -34.1590954 0.54 -497.3049058 -0.0926936 -497.3975994 0.86
CONF5 -34.1589250 0.65 -497.3056747 -0.0932887 -497.3989634 0.00 <------
CONF6 -34.1587465 0.76 -497.3049670 -0.0927849 -497.3977519 0.76
CONF7 -34.1578065 1.35 -497.2983644 -0.0945716 -497.3929360 3.78
CONF8 -34.1571241 1.78 -497.3029570 -0.0927525 -497.3957096 2.04
CONF9 -34.1570372 1.83 -497.3008248 -0.0931616 -497.3939864 3.12
CONF10 -34.1563217 2.28 -497.3038986 -0.0911699 -497.3950685 2.44
CONF11 -34.1559251 2.53 -497.3008250 -0.0934858 -497.3943108 2.92
CONF12 -34.1554750 2.81 -497.3045828 -0.0890026 -497.3935854 3.37
CONF13 -34.1554585 2.82 -497.3036749 -0.0899805 -497.3936554 3.33
CONF14 -34.1537285 3.91 -497.3022176 -0.0912277 -497.3934453 3.46
CONF15 -34.1529637 4.39 -497.3009381 -0.0927229 -497.3936610 3.33
CONF16 -34.1514138 5.36 -497.3063638 -0.0850983 -497.3914621 4.71
CONF17 -34.1512255 5.48 -497.3047147 -0.0859828 -497.3906975 5.19
CONF18 -34.1510249 5.60 -497.2564102 -0.1322422 -497.3886524 6.47
CONF19 -34.1509627 5.64 -497.2746319 -0.1105730 -497.3852050 8.63
CONF20 -34.1508506 5.71 -497.2550494 -0.1322369 -497.3872863 7.33
CONF21 -34.1504892 5.94 -497.2896633 -0.0991503 -497.3888135 6.37
CONF22 -34.1504331 5.98 -497.2596139 -0.1253634 -497.3849773 8.78
--------------------------------------------------
Conformers considered further
--------------------------------------------------
Below the g_thr(1) threshold of 3.5 kcal/mol.
CONF1, CONF2, CONF3, CONF4, CONF5, CONF6, CONF8, CONF9, CONF10, CONF11, CONF12
CONF13, CONF14, CONF15
--------------------------------------------------
Calculating prescreening G_mRRHO with implicit solvation!
The prescreening G_mRRHO calculation is now performed for:
CONF1, CONF2, CONF3, CONF4, CONF5, CONF6, CONF8, CONF9, CONF10, CONF11, CONF12
CONF13, CONF14, CONF15
Constructed folders!
Starting 14 G_RRHO calculations.
Running GFN2-xTB mRRHO in CONF1/rrho_part1
Running GFN2-xTB mRRHO in CONF2/rrho_part1
Running GFN2-xTB mRRHO in CONF3/rrho_part1
Running GFN2-xTB mRRHO in CONF4/rrho_part1
Running GFN2-xTB mRRHO in CONF5/rrho_part1
Running GFN2-xTB mRRHO in CONF6/rrho_part1
Running GFN2-xTB mRRHO in CONF8/rrho_part1
Running GFN2-xTB mRRHO in CONF9/rrho_part1
Running GFN2-xTB mRRHO in CONF10/rrho_part1
Running GFN2-xTB mRRHO in CONF11/rrho_part1
Running GFN2-xTB mRRHO in CONF12/rrho_part1
Running GFN2-xTB mRRHO in CONF13/rrho_part1
Running GFN2-xTB mRRHO in CONF14/rrho_part1
Running GFN2-xTB mRRHO in CONF15/rrho_part1
Tasks completed!
The prescreening G_mRRHO calculation @ c1 was successful for CONF1/rrho_part1: 0.18236493
The prescreening G_mRRHO calculation @ c1 was successful for CONF2/rrho_part1: 0.18246714
The prescreening G_mRRHO calculation @ c1 was successful for CONF3/rrho_part1: 0.18235782
The prescreening G_mRRHO calculation @ c1 was successful for CONF4/rrho_part1: 0.18239049
The prescreening G_mRRHO calculation @ c1 was successful for CONF5/rrho_part1: 0.18241907
The prescreening G_mRRHO calculation @ c1 was successful for CONF6/rrho_part1: 0.18225430
The prescreening G_mRRHO calculation @ c1 was successful for CONF8/rrho_part1: 0.18193879
The prescreening G_mRRHO calculation @ c1 was successful for CONF9/rrho_part1: 0.18214342
The prescreening G_mRRHO calculation @ c1 was successful for CONF10/rrho_part1: 0.18217367
The prescreening G_mRRHO calculation @ c1 was successful for CONF11/rrho_part1: 0.18267361
The prescreening G_mRRHO calculation @ c1 was successful for CONF12/rrho_part1: 0.18167483
The prescreening G_mRRHO calculation @ c1 was successful for CONF13/rrho_part1: 0.18145764
The prescreening G_mRRHO calculation @ c1 was successful for CONF14/rrho_part1: 0.18268845
The prescreening G_mRRHO calculation @ c1 was successful for CONF15/rrho_part1: 0.18320604
--------------------------------------------------
* Gibbs free energies of part1 *
--------------------------------------------------
CONF# G(GFNn-xTB) ΔG(GFNn-xTB) E [Eh] Gsolv [Eh] GmRRHO [Eh] Gtot ΔGtot
[a.u.] [kcal/mol] r2scan-3c COSMO-RS-normal GFN2 [Eh] [kcal/mol]
[r2scan-3c] [alpb]-bhess
CONF1 -33.9775899 0.00 -497.3021467 -0.0939108 0.1823649 -497.2136926 1.79
CONF2 -33.9769813 0.38 -497.3049956 -0.0934472 0.1824671 -497.2159757 0.36
CONF3 -33.9768952 0.44 -497.3064930 -0.0918917 0.1823578 -497.2160268 0.32
CONF4 -33.9767049 0.56 -497.3049058 -0.0926936 0.1823905 -497.2152089 0.84
CONF5 -33.9765060 0.68 -497.3056747 -0.0932887 0.1824191 -497.2165444 0.00 <------
CONF6 -33.9764922 0.69 -497.3049670 -0.0927849 0.1822543 -497.2154976 0.66
CONF8 -33.9751853 1.51 -497.3029570 -0.0927525 0.1819388 -497.2137708 1.74
CONF9 -33.9748938 1.69 -497.3008248 -0.0931616 0.1821434 -497.2118430 2.95
CONF10 -33.9741480 2.16 -497.3038986 -0.0911699 0.1821737 -497.2128948 2.29
CONF11 -33.9732515 2.72 -497.3008250 -0.0934858 0.1826736 -497.2116372 3.08
CONF12 -33.9738002 2.38 -497.3045828 -0.0890026 0.1816748 -497.2119106 2.91
CONF13 -33.9740008 2.25 -497.3036749 -0.0899805 0.1814576 -497.2121977 2.73
CONF14 -33.9710400 4.11 -497.3022176 -0.0912277 0.1826885 -497.2107568 3.63
CONF15 -33.9697576 4.91 -497.3009381 -0.0927229 0.1832060 -497.2104549 3.82
Additional global 'fuzzy-threshold' based on the standard deviation of (G_mRRHO):
Std_dev(G_mRRHO) = 0.272 kcal/mol
Fuzzythreshold = 0.309 kcal/mol
Final sorting threshold G_thr(1) = 3.500 + 0.309 = 3.809 kcal/mol
Spearman correlation coefficient between (E + Solv) and (E + Solv + mRRHO) = 0.908
--------------------------------------------------
Conformers considered further
--------------------------------------------------
Considered CONF14 because of increased fuzzythr.
These conformers are below the 3.809 kcal/mol G_thr(1) threshold.
CONF1, CONF2, CONF3, CONF4, CONF5, CONF6, CONF8, CONF9, CONF10, CONF11, CONF12
CONF13, CONF14
Calculating Boltzmann averaged free energy of ensemble on input geometries (not DFT optimized)!
temperature /K: avE(T) /a.u. avGmRRHO(T) /a.u. avGsolv(T) /a.u. avG(T) /a.u.
----------------------------------------------------------------------------------------------------
298.15 -497.3054054 0.1823775 -0.0928881 -497.2159160 <<==part1==
----------------------------------------------------------------------------------------------------
Calculating unbiased GFNn-xTB energy
Constructed folders!
Starting 13 xTB - single-point calculations.
gfn2-xTB energy for CONF1/GFN_unbiased = -34.1515395
gfn2-xTB energy for CONF2/GFN_unbiased = -34.1509941
gfn2-xTB energy for CONF3/GFN_unbiased = -34.1515326
gfn2-xTB energy for CONF4/GFN_unbiased = -34.1508491
gfn2-xTB energy for CONF5/GFN_unbiased = -34.1514366
gfn2-xTB energy for CONF6/GFN_unbiased = -34.1512893
gfn2-xTB energy for CONF8/GFN_unbiased = -34.1493072
gfn2-xTB energy for CONF9/GFN_unbiased = -34.1491025
gfn2-xTB energy for CONF10/GFN_unbiased = -34.1491972
gfn2-xTB energy for CONF11/GFN_unbiased = -34.1487085
gfn2-xTB energy for CONF12/GFN_unbiased = -34.1484725
gfn2-xTB energy for CONF13/GFN_unbiased = -34.1480733
gfn2-xTB energy for CONF14/GFN_unbiased = -34.1461266
Tasks completed!
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>END of Part1<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
Ran part1 in 277.0194 seconds
Part : #conf time
--------------------------------------------------
Input : 22 -
Part1_initial_sort : 14 -
Part1_all : 14 277.02s
--------------------------------------------------
All parts : 277.02s
CENSO all done!
$CENSO global configuration file: .censorc
$VERSION:1.0.3
ORCA: /home/USER/orca_4_2_1_linux_x86-64_openmpi216
ORCA version: 4.2.1
GFN-xTB: xtb
CREST: crest
mpshift: mpshift
escf: escf
#COSMO-RS
ctd = BP_TZVPD_FINE_C30_1601.ctd cdir = "/home/USER/COSMOlogic/COSMOthermX19/COSMOtherm/CTDATA-FILES" ldir = "/home/USER/COSMOlogic/COSMOthermX19/COSMOtherm/CTDATA-FILES"
cosmothermversion: 19
$ENDPROGRAMS
$CRE SORTING SETTINGS:
$GENERAL SETTINGS:
nconf: all # ['all', 'number e.g. 10 up to all conformers']
charge: 0 # ['number e.g. 0']
unpaired: 0 # ['number e.g. 0']
solvent: gas # ['gas', 'acetone', 'chcl3', 'acetonitrile', 'ch2cl2', 'dmso', 'h2o', 'methanol', 'thf', '...']
prog_rrho: xtb # ['xtb', 'prog']
temperature: 298.15 # ['temperature in K e.g. 298.15']
trange: [273.15, 378.15, 5] # ['temperature range [start, end, step]']
multitemp: on # ['on', 'off']
evaluate_rrho: on # ['on', 'off']
consider_sym: off # ['on', 'off']
bhess: on # ['on', 'off']
imagthr: automatic # ['automatic or e.g., -100 # in cm-1']
sthr: automatic # ['automatic or e.g., 50 # in cm-1']
scale: automatic # ['automatic or e.g., 1.0 ']
rmsdbias: off # ['on', 'off']
sm_rrho: alpb # ['alpb', 'gbsa']
check: on # ['on', 'off']
prog: tm # ['tm', 'orca']
func: r2scan-3c # ['pbe', 'b97-d', 'pbeh-3c', 'tpss', 'b97-d3', 'r2scan-3c', 'b97-3c']
basis: automatic # ['automatic', 'def2-mSVP', 'def2-mTZVP', 'def2-mTZVP', 'def2-TZVP', '...']
maxthreads: 2 # ['number of threads e.g. 2']
omp: 2 # ['number cores per thread e.g. 4']
cosmorsparam: automatic # ['automatic', '12-fine', '12-normal', '13-fine', '13-normal', '14-fine', '...']
$PART0 - CHEAP-PRESCREENING - SETTINGS:
part0: off # ['on', 'off']
func0: b97-d # ['pbeh-3c', 'b97-3c', 'b97-d3', 'pbe', 'r2scan-3c', 'tpss', 'b97-d']
basis0: def2-SV(P) # ['automatic', 'def2-mSVP', 'def2-mTZVP', 'def2-mTZVP', 'def2-TZVP', '...']
part0_gfnv: gfn2 # ['gfn1', 'gfn2', 'gfnff']
part0_threshold: 4.0 # ['number e.g. 4.0']
$PART1 - PRESCREENING - SETTINGS:
# func and basis is set under GENERAL SETTINGS
part1: off # ['on', 'off']
smgsolv1: cosmors # ['alpb_gsolv', 'dcosmors', 'cosmo', 'smd', 'cosmors-fine', 'cpcm', 'gbsa_gsolv', '...']
part1_gfnv: gfn2 # ['gfn1', 'gfn2', 'gfnff']
part1_threshold: 3.5 # ['number e.g. 5.0']
$PART2 - OPTIMIZATION - SETTINGS:
# func and basis is set under GENERAL SETTINGS
part2: off # ['on', 'off']
opt_limit: 2.5 # ['number e.g. 4.0']
sm2: dcosmors # ['cosmo', 'cpcm', 'default', 'smd', 'dcosmors']
smgsolv2: cosmors # ['cosmors-fine', 'gbsa_gsolv', 'cosmo', 'cpcm', 'smd_gsolv', 'alpb_gsolv', 'smd', '...']
part2_gfnv: gfn2 # ['gfn1', 'gfn2', 'gfnff']
ancopt: on # ['on']
hlow: 0.01 # ['lowest force constant in ANC generation, e.g. 0.01']
opt_spearman: on # ['on', 'off']
part2_threshold: 99 # ['Boltzmann sum threshold in %. e.g. 95 (between 1 and 100)']
optlevel2: automatic # ['crude', 'sloppy', 'loose', 'lax', 'normal', 'tight', 'vtight', 'extreme', '...']
optcycles: 8 # ['number e.g. 5 or 10']
spearmanthr: -4.0 # ['value between -1 and 1, if outside set automatically']
radsize: 10 # ['number e.g. 8 or 10']
crestcheck: off # ['on', 'off']
$PART3 - REFINEMENT - SETTINGS:
part3: off # ['on', 'off']
prog3: prog # ['tm', 'orca', 'prog']
func3: pw6b95 # ['dsd-blyp', 'pw6b95', 'b97-d3', 'r2scan-3c', 'pbe0', 'wb97x']
basis3: def2-TZVPD # ['SVP', 'SV(P)', 'TZVP', 'TZVPP', 'QZVP', 'QZVPP', 'def2-SV(P)', 'def2-mSVP', '...']
smgsolv3: cosmors # ['alpb_gsolv', 'dcosmors', 'cosmo', 'smd', 'cosmors-fine', 'cpcm', 'gbsa_gsolv', '...']
part3_gfnv: gfn2 # ['gfn1', 'gfn2', 'gfnff']
part3_threshold: 99 # ['Boltzmann sum threshold in %. e.g. 95 (between 1 and 100)']
$NMR PROPERTY SETTINGS:
$PART4 SETTINGS:
part4: off # ['on', 'off']
couplings: on # ['on', 'off']
progJ: prog # ['tm', 'orca', 'adf', 'prog']
funcJ: pbe0 # ['tpss', 'pbe0', 'pbeh-3c']
basisJ: def2-TZVP # ['SVP', 'SV(P)', 'TZVP', 'TZVPP', 'QZVP', 'QZVPP', 'def2-SV(P)', 'def2-mSVP', '...']
sm4J: default # ['dcosmors', 'smd', 'cosmo', 'cpcm']
shieldings: on # ['on', 'off']
progS: prog # ['tm', 'orca', 'adf', 'prog']
funcS: pbe0 # ['dsd-blyp', 'pbeh-3c', 'tpss', 'pbe0', 'kt2']
basisS: def2-TZVP # ['SVP', 'SV(P)', 'TZVP', 'TZVPP', 'QZVP', 'QZVPP', 'def2-SV(P)', 'def2-mSVP', '...']
sm4S: default # ['dcosmors', 'smd', 'cosmo', 'cpcm']
reference_1H: TMS # ['TMS']
reference_13C: TMS # ['TMS']
reference_19F: CFCl3 # ['CFCl3']
reference_29Si: TMS # ['TMS']
reference_31P: TMP # ['TMP', 'PH3']
1H_active: on # ['on', 'off']
13C_active: on # ['on', 'off']
19F_active: off # ['on', 'off']
29Si_active: off # ['on', 'off']
31P_active: off # ['on', 'off']
resonance_frequency: 300.0 # ['MHz number of your experimental spectrometer setup']
$OPTICAL ROTATION PROPERTY SETTINGS:
$PART5 SETTINGS:
optical_rotation: off # ['on', 'off']
funcOR: pbe # ['functional for opt_rot e.g. pbe']
funcOR_SCF: r2scan-3c # ['functional for SCF in opt_rot e.g. r2scan-3c']
basisOR: def2-SVPD # ['basis set for opt_rot e.g. def2-SVPD']
frequency_optical_rot: [589.0] # ['list of freq in nm to evaluate opt rot at e.g. [589, 700]']
$END CENSORC
25
-34.15995484
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25
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25
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25
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25
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25
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H 4.3101055621 -1.0795234870 -0.6518667702
H 3.4997443822 -0.1538144186 -1.7841531054
H 5.0842467659 0.2120203831 -1.3873716549
H -1.8037773550 1.6476905491 -1.6249441216
25
-34.15048917
O -1.9774584219 -0.8822136242 -1.3447844876
O -0.7353222350 -1.3040874260 0.4712779300
N -1.2018711229 0.8204001109 1.6759883927
N 1.9464051556 -1.6923491374 0.3496868798
C 0.8058411616 1.0462579377 -0.9468506072
C -0.4754178942 1.7785998054 -0.5275051890
C 1.8226970853 0.7789686777 0.1752315710
C -1.5019161161 0.9155320919 0.2220611780
C 2.6576744598 -0.4659344426 -0.1177787426
C -1.4255171488 -0.5796126398 -0.2987743324
H 1.2927227489 1.6467822241 -1.7161034319
H 0.5115436171 0.1136959367 -1.4299162738
H -0.9626535770 2.1244807715 -1.4395462399
H -0.2313854006 2.6631384020 0.0636669169
H 2.4836824282 1.6401220787 0.2631946203
H 1.3379895832 0.6415415675 1.1385387246
H -2.5044279955 1.3042479639 0.0511624497
H 3.6220420553 -0.4105315490 0.3870533340
H 2.8346807725 -0.5412209492 -1.1903941633
H -0.5537202797 1.5469435382 2.0029686770
H -2.0510266978 0.8448716653 2.2497725116
H 0.8939724574 -1.6086997720 0.2334441992
H 2.2630899289 -2.5235198565 -0.1606712473
H 2.1155048181 -1.8450780227 1.3513380594
H -0.7798223195 -0.1709536166 1.7101046448
25
-34.15043307
O -3.3078583007 -0.3518099727 0.5480566241
O -1.8441149941 -2.0073969491 0.1397595703
N -1.9672328473 1.5403727742 -0.2372000800
N 3.6044925126 -0.8358440764 -0.6659647320
C 1.1684565146 1.0446332415 -0.4943940738
C 0.1082467096 0.2177955398 0.2395309885
C 2.4785715426 1.1657908669 0.2896724500
C -1.2458520269 0.2676289576 -0.4513144135
C 3.1696429470 -0.1592315605 0.5890169973
C -2.2263428078 -0.8414226742 0.1422529421
H 0.7932826990 2.0569151989 -0.6482792542
H 1.3354698371 0.6191303209 -1.4843783659
H -0.0031461344 0.5661490514 1.2686433794
H 0.3791631733 -0.8378892566 0.2841197320
H 3.1579098277 1.8188328559 -0.2597110183
H 2.2713923792 1.6478155935 1.2450536588
H -1.1432114953 0.0569418065 -1.5170262136
H 2.5004236326 -0.8240708177 1.1341470919
H 4.0493855213 0.0280822082 1.2049984895
H -1.5070190112 2.1488324010 0.4454597884
H -2.1837208522 2.0584218679 -1.0901715209
H 4.2094106392 -0.2068158824 -1.2153183037
H 4.1256865653 -1.6973771969 -0.4514692989
H 2.7834959501 -1.0854874671 -1.2358687369
H -2.8845837684 1.1083956166 0.2016053653
Calculate free energies on populated, DFT optimized conformers¶
Note
Using sorting parts: part0 and part1 in order to reduce the number of computational costly DFT geometry optimizations
example settings are read from .censorc file
$ censo -inp ensemble.xyz -inprc /path/to/.censorc > censo.out &
______________________________________________________________
| |
| |
| CENSO - Commandline ENSO |
| v 1.0.3 |
| energetic sorting of CREST Conformer Rotamer Ensembles |
| University of Bonn, MCTC |
| Feb 2021 |
| based on ENSO version 2.0.1 |
| F. Bohle and S. Grimme |
| |
|______________________________________________________________|
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
----------------------------------------------------------------------------------------------------
PARAMETERS
----------------------------------------------------------------------------------------------------
The configuration file .censorc is read from /home/bohle/1projects/from_tmp1/CENSO/documentation-calcs/3-part0-2/.censorc.
Reading conformer rotamer ensemble from: /home/bohle/1projects/from_tmp1/CENSO/documentation-calcs/3-part0-2/ensemble.xyz.
Reading file: censo_solvents.json
--------------------------------------------------
CRE SORTING SETTINGS
--------------------------------------------------
number of atoms in system: 25
number of considered conformers: 22
number of all conformers from input: 22
charge: 1
unpaired: 0
solvent: h2o
temperature: 298.15
evaluate at different temperatures: on
temperature range: 273.15, 278.15, 283.15, 288.15, ...
calculate mRRHO contribution: on
consider symmetry for mRRHO contribution: off
cautious checking for error and failed calculations: on
checking the DFT-ensemble using CREST: off
maxthreads: 4
omp: 2
--------------------------------------------------
CRE CHEAP-PRESCREENING - PART0
--------------------------------------------------
part0: on
starting number of considered conformers: 22
program for part0: tm
functional for fast single-point: b97-d
basis set for fast single-point: def2-SV(P)
threshold g_thr(0) for sorting in part0: 4.0
Solvent model used with xTB: alpb
short-notation:
b97-d-D3/def2-SV(P) // GFNn-xTB (Input geometry)
--------------------------------------------------
CRE PRESCREENING - PART1
--------------------------------------------------
part1: on
starting number of considered conformers: 22
program for part1: tm
functional for initial evaluation: r2scan-3c
basis set for initial evaluation: def2-mTZVPP
calculate mRRHO contribution: on
program for mRRHO contribution: xtb
GFN version for mRRHO and/or GBSA_Gsolv: gfn2
Apply constraint to input geometry during mRRHO calculation: on
solvent model applied with xTB: alpb
evaluate at different temperatures: off
threshold g_thr(1) and G_thr(1) for sorting in part1: 3.5
solvent model for Gsolv contribution of part1: cosmors
short-notation:
r2scan-3c + COSMORS[h2o] + GmRRHO(GFN2[alpb]-bhess) // GFNn-xTB (Input geometry)
--------------------------------------------------
CRE OPTIMIZATION - PART2
--------------------------------------------------
part2: on
program: tm
functional for part2: r2scan-3c
basis set for part2: def2-mTZVPP
using xTB-optimizer for optimization: on
using the new ensemble optimizer: on
optimize all conformers below this G_thr(opt,2) threshold: 2.5
spearmanthr: 0.935
optimization level in part2: lax
solvent model applied in the optimization: dcosmors
solvent model for Gsolv contribution: cosmors
evaluate at different temperatures: on
Boltzmann sum threshold G_thr(2) for sorting in part2: 99.0
calculate mRRHO contribution: on
program for mRRHO contribution: xtb
GFN version for mRRHO and/or GBSA_Gsolv: gfn2
Apply constraint to input geometry during mRRHO calculation: on
solvent model applied with xTB: alpb
short-notation:
r2scan-3c + COSMORS[h2o] + GmRRHO(GFN2[alpb]-bhess) // r2scan-3c[DCOSMORS]
END of parameters
------------------------------------------------------------
PATHS of external QM programs
------------------------------------------------------------
The following program paths are used:
xTB: /home/abt-grimme/AK-bin/xtb
TURBOMOLE: /home/abt-grimme/TURBOMOLE.7.5.1/bin/em64t-unknown-linux-gnu_smp
Setup of COSMO-RS:
ctd = BP_TZVPD_FINE_C30_1601.ctd
cdir = "/home/bohle/COSMOlogic/COSMOthermX19/COSMOtherm/CTDATA-FILES"
ldir = "/home/bohle/COSMOlogic/COSMOthermX19/COSMOtherm/CTDATA-FILES"
Using /home/bohle/COSMOlogic/COSMOthermX19/COSMOtherm/DATABASE-COSMO/BP-TZVP-COSMO
as path to the COSMO-RS NORMAL DATABASE.
Using cefine from /home/bohle/bin/cefine
PARNODES for TM or COSMO-RS calculation was set to 2
Using COSMOtherm from /home/bohle/COSMOlogic/COSMOthermX19/COSMOtherm/BIN-LINUX/cosmotherm
----------------------------------------------------------------------------------------------------
Processing data from previous run (enso.json)
----------------------------------------------------------------------------------------------------
INFORMATION: No restart information exists and is created during this run!
----------------------------------------------------------------------------------------------------
CRE CHEAP-PRESCREENING - PART0
----------------------------------------------------------------------------------------------------
program: tm
functional for part0: b97-d
basis set for part0: def2-SV(P)
threshold g_thr(0): 4.0
starting number of considered conformers: 22
Calculating efficient gas-phase single-point energies:
The efficient gas-phase single-point is calculated for:
CONF1, CONF2, CONF3, CONF4, CONF5, CONF6, CONF7, CONF8, CONF9, CONF10, CONF11
CONF12, CONF13, CONF14, CONF15, CONF16, CONF17, CONF18, CONF19, CONF20, CONF21, CONF22
Constructed folders!
Starting 22 ALPB-Gsolv calculations
Running single-point in CONF1/part0_sp
Running single-point in CONF2/part0_sp
Running single-point in CONF3/part0_sp
Running single-point in CONF4/part0_sp
Running ALPB_GSOLV calculation in 3-part0-2/CONF1/part0_sp
Running ALPB_GSOLV calculation in 3-part0-2/CONF3/part0_sp
Running ALPB_GSOLV calculation in 3-part0-2/CONF2/part0_sp
Running ALPB_GSOLV calculation in 3-part0-2/CONF4/part0_sp
Running single-point in CONF5/part0_sp
Running single-point in CONF6/part0_sp
Running single-point in CONF7/part0_sp
Running single-point in CONF8/part0_sp
Running ALPB_GSOLV calculation in 3-part0-2/CONF5/part0_sp
Running ALPB_GSOLV calculation in 3-part0-2/CONF6/part0_sp
Running ALPB_GSOLV calculation in 3-part0-2/CONF7/part0_sp
Running ALPB_GSOLV calculation in 3-part0-2/CONF8/part0_sp
Running single-point in CONF9/part0_sp
Running single-point in CONF11/part0_sp
Running single-point in CONF10/part0_sp
Running single-point in CONF12/part0_sp
Running ALPB_GSOLV calculation in 3-part0-2/CONF9/part0_sp
Running ALPB_GSOLV calculation in 3-part0-2/CONF10/part0_sp
Running ALPB_GSOLV calculation in 3-part0-2/CONF11/part0_sp
Running ALPB_GSOLV calculation in 3-part0-2/CONF12/part0_sp
Running single-point in CONF13/part0_sp
Running single-point in CONF15/part0_sp
Running single-point in CONF14/part0_sp
Running single-point in CONF16/part0_sp
Running ALPB_GSOLV calculation in 3-part0-2/CONF13/part0_sp
Running ALPB_GSOLV calculation in 3-part0-2/CONF15/part0_sp
Running ALPB_GSOLV calculation in 3-part0-2/CONF14/part0_sp
Running single-point in CONF17/part0_sp
Running ALPB_GSOLV calculation in 3-part0-2/CONF16/part0_sp
Running single-point in CONF18/part0_sp
Running single-point in CONF19/part0_sp
Running ALPB_GSOLV calculation in 3-part0-2/CONF17/part0_sp
Running single-point in CONF20/part0_sp
Running ALPB_GSOLV calculation in 3-part0-2/CONF18/part0_sp
Running ALPB_GSOLV calculation in 3-part0-2/CONF19/part0_sp
Running single-point in CONF21/part0_sp
Running single-point in CONF22/part0_sp
Running ALPB_GSOLV calculation in 3-part0-2/CONF20/part0_sp
Running ALPB_GSOLV calculation in 3-part0-2/CONF22/part0_sp
Running ALPB_GSOLV calculation in 3-part0-2/CONF21/part0_sp
Tasks completed!
The efficient gas-phase single-point was successful for CONF1/part0_sp: E(DFT) = -496.55110270 Gsolv = -0.12279245
The efficient gas-phase single-point was successful for CONF2/part0_sp: E(DFT) = -496.55473079 Gsolv = -0.12241044
The efficient gas-phase single-point was successful for CONF3/part0_sp: E(DFT) = -496.55551554 Gsolv = -0.12099969
The efficient gas-phase single-point was successful for CONF4/part0_sp: E(DFT) = -496.55384665 Gsolv = -0.12156811
The efficient gas-phase single-point was successful for CONF5/part0_sp: E(DFT) = -496.55341065 Gsolv = -0.12251050
The efficient gas-phase single-point was successful for CONF6/part0_sp: E(DFT) = -496.55368828 Gsolv = -0.12175678
The efficient gas-phase single-point was successful for CONF7/part0_sp: E(DFT) = -496.54759208 Gsolv = -0.12365913
The efficient gas-phase single-point was successful for CONF8/part0_sp: E(DFT) = -496.55118920 Gsolv = -0.12200372
The efficient gas-phase single-point was successful for CONF9/part0_sp: E(DFT) = -496.54970422 Gsolv = -0.12167549
The efficient gas-phase single-point was successful for CONF10/part0_sp: E(DFT) = -496.55157272 Gsolv = -0.12001541
The efficient gas-phase single-point was successful for CONF11/part0_sp: E(DFT) = -496.54991969 Gsolv = -0.12296934
The efficient gas-phase single-point was successful for CONF12/part0_sp: E(DFT) = -496.55212770 Gsolv = -0.11751864
The efficient gas-phase single-point was successful for CONF13/part0_sp: E(DFT) = -496.55077718 Gsolv = -0.11854291
The efficient gas-phase single-point was successful for CONF14/part0_sp: E(DFT) = -496.55028792 Gsolv = -0.12090071
The efficient gas-phase single-point was successful for CONF15/part0_sp: E(DFT) = -496.54987374 Gsolv = -0.12311773
The efficient gas-phase single-point was successful for CONF16/part0_sp: E(DFT) = -496.55360018 Gsolv = -0.11274054
The efficient gas-phase single-point was successful for CONF17/part0_sp: E(DFT) = -496.55289531 Gsolv = -0.11378052
The efficient gas-phase single-point was successful for CONF18/part0_sp: E(DFT) = -496.50423172 Gsolv = -0.16468285
The efficient gas-phase single-point was successful for CONF19/part0_sp: E(DFT) = -496.52384365 Gsolv = -0.14390846
The efficient gas-phase single-point was successful for CONF20/part0_sp: E(DFT) = -496.50481476 Gsolv = -0.16519450
The efficient gas-phase single-point was successful for CONF21/part0_sp: E(DFT) = -496.53860751 Gsolv = -0.13212346
The efficient gas-phase single-point was successful for CONF22/part0_sp: E(DFT) = -496.50938650 Gsolv = -0.15826546
----------------------------------------------------------------------------------------------------
Removing high lying conformers by improved energy description
----------------------------------------------------------------------------------------------------
CONF# G [Eh] ΔG [kcal/mol] E [Eh] Gsolv [Eh] Gtot ΔE(DFT) ΔGsolv ΔGtot
GFN2-xTB GFN2-xTB b97-d-D3(0)/def2-SV(P) alpb [Eh] [kcal/mol] [kcal/mol] [kcal/mol]
[ALPB] [ALPB] [gfn2]
CONF1 -34.1746819 0.00 -496.5511027 -0.1227924 -496.6738951 2.28 -0.24 2.04
CONF2 -34.1743917 0.18 -496.5547308 -0.1224104 -496.6771412 0.00 0.00 0.00 <------
CONF3 -34.1742792 0.25 -496.5555155 -0.1209997 -496.6765152 -0.49 0.89 0.39
CONF4 -34.1739821 0.44 -496.5538467 -0.1215681 -496.6754148 0.55 0.53 1.08
CONF5 -34.1740224 0.41 -496.5534106 -0.1225105 -496.6759212 0.83 -0.06 0.77
CONF6 -34.1736309 0.66 -496.5536883 -0.1217568 -496.6754451 0.65 0.41 1.06
CONF7 -34.1725555 1.33 -496.5475921 -0.1236591 -496.6712512 4.48 -0.78 3.70
CONF8 -34.1721876 1.57 -496.5511892 -0.1220037 -496.6731929 2.22 0.26 2.48
CONF9 -34.1719439 1.72 -496.5497042 -0.1216755 -496.6713797 3.15 0.46 3.62
CONF10 -34.1714765 2.01 -496.5515727 -0.1200154 -496.6715881 1.98 1.50 3.48
CONF11 -34.1712638 2.14 -496.5499197 -0.1229693 -496.6728890 3.02 -0.35 2.67
CONF12 -34.1704841 2.63 -496.5521277 -0.1175186 -496.6696463 1.63 3.07 4.70
CONF13 -34.1703687 2.71 -496.5507772 -0.1185429 -496.6693201 2.48 2.43 4.91
CONF14 -34.1694191 3.30 -496.5502879 -0.1209007 -496.6711886 2.79 0.95 3.74
CONF15 -34.1691431 3.48 -496.5498737 -0.1231177 -496.6729915 3.05 -0.44 2.60
CONF16 -34.1664418 5.17 -496.5536002 -0.1127405 -496.6663407 0.71 6.07 6.78
CONF17 -34.1661652 5.34 -496.5528953 -0.1137805 -496.6666758 1.15 5.42 6.57
CONF18 -34.1660003 5.45 -496.5042317 -0.1646828 -496.6689146 31.69 -26.53 5.16
CONF19 -34.1664801 5.15 -496.5238437 -0.1439085 -496.6677521 19.38 -13.49 5.89
CONF20 -34.1658387 5.55 -496.5048148 -0.1651945 -496.6700093 31.32 -26.85 4.48
CONF21 -34.1670164 4.81 -496.5386075 -0.1321235 -496.6707310 10.12 -6.10 4.02
CONF22 -34.1656180 5.69 -496.5093865 -0.1582655 -496.6676520 28.45 -22.50 5.95
----------------------------------------------------------------------------------------------------
--------------------------------------------------
Conformers considered further
--------------------------------------------------
These conformers are below the 4.000 kcal/mol g_thr(0) threshold.
CONF1, CONF2, CONF3, CONF4, CONF5, CONF6, CONF7, CONF8, CONF9, CONF10, CONF11
CONF14, CONF15
Calculating Boltzmann averaged (free) energy of ensemble on input geometries (not DFT optimized)!
temperature /K: avE(T) /a.u. avG(T) /a.u.
----------------------------------------------------------------------------------------------------
298.15 -496.5544580 -496.6764445 <<==part0==
----------------------------------------------------------------------------------------------------
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>END of Part0<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
Ran part0 in 25.3156 seconds
----------------------------------------------------------------------------------------------------
CRE PRESCREENING - PART1
----------------------------------------------------------------------------------------------------
program: tm
functional for part1 and 2: r2scan-3c
basis set for part1 and 2: def2-mTZVPP
Solvent: h2o
solvent model for Gsolv contribution: cosmors
threshold g_thr(1) and G_thr(1): 3.5
starting number of considered conformers: 13
calculate mRRHO contribution: on
program for mRRHO contribution: xtb
GFN version for mRRHO and/or GBSA_Gsolv: gfn2
Apply constraint to input geometry during mRRHO calculation: on
temperature: 298.15
Calculating single-point energies and solvation contribution (G_solv):
The prescreening COSMO-RS is calculated for:
CONF1, CONF2, CONF3, CONF4, CONF5, CONF6, CONF7, CONF8, CONF9, CONF10, CONF11
CONF14, CONF15
Constructed folders!
Constructed folders!
Starting 13 COSMO-RS-Gsolv calculations.
Running COSMO-RS calculation in CONF1/r2scan-3c/COSMO
Running COSMO-RS calculation in CONF2/r2scan-3c/COSMO
Running COSMO-RS calculation in CONF3/r2scan-3c/COSMO
Running COSMO-RS calculation in CONF4/r2scan-3c/COSMO
Running COSMO-RS calculation in CONF5/r2scan-3c/COSMO
Running COSMO-RS calculation in CONF6/r2scan-3c/COSMO
Running COSMO-RS calculation in CONF7/r2scan-3c/COSMO
Running COSMO-RS calculation in CONF8/r2scan-3c/COSMO
Running COSMO-RS calculation in CONF9/r2scan-3c/COSMO
Running COSMO-RS calculation in CONF10/r2scan-3c/COSMO
Running COSMO-RS calculation in CONF11/r2scan-3c/COSMO
Running COSMO-RS calculation in CONF14/r2scan-3c/COSMO
Running COSMO-RS calculation in CONF15/r2scan-3c/COSMO
Tasks completed!
prescreening COSMO-RS calculation was successful for CONF1/r2scan-3c/COSMO: -0.10999518
prescreening COSMO-RS calculation was successful for CONF2/r2scan-3c/COSMO: -0.10920229
prescreening COSMO-RS calculation was successful for CONF3/r2scan-3c/COSMO: -0.10753681
prescreening COSMO-RS calculation was successful for CONF4/r2scan-3c/COSMO: -0.10829026
prescreening COSMO-RS calculation was successful for CONF5/r2scan-3c/COSMO: -0.10936797
prescreening COSMO-RS calculation was successful for CONF6/r2scan-3c/COSMO: -0.10838241
prescreening COSMO-RS calculation was successful for CONF7/r2scan-3c/COSMO: -0.11058677
prescreening COSMO-RS calculation was successful for CONF8/r2scan-3c/COSMO: -0.10882956
prescreening COSMO-RS calculation was successful for CONF9/r2scan-3c/COSMO: -0.10889910
prescreening COSMO-RS calculation was successful for CONF10/r2scan-3c/COSMO: -0.10665800
prescreening COSMO-RS calculation was successful for CONF11/r2scan-3c/COSMO: -0.10960927
prescreening COSMO-RS calculation was successful for CONF14/r2scan-3c/COSMO: -0.10711489
prescreening COSMO-RS calculation was successful for CONF15/r2scan-3c/COSMO: -0.10994652
--------------------------------------------------
Removing high lying conformers
--------------------------------------------------
CONF# E(GFNn-xTB) ΔE(GFNn-xTB) E [Eh] Gsolv [Eh] Gtot ΔGtot
[a.u.] [kcal/mol] r2scan-3c COSMO-RS-normal [Eh] [kcal/mol]
[r2scan-3c]
CONF1 -34.1599548 0.00 -497.3021467 -0.1099952 -497.4121419 1.82
CONF2 -34.1594484 0.32 -497.3049956 -0.1092023 -497.4141979 0.53
CONF3 -34.1592530 0.44 -497.3064930 -0.1075368 -497.4140298 0.64
CONF4 -34.1590954 0.54 -497.3049058 -0.1082903 -497.4131961 1.16
CONF5 -34.1589250 0.65 -497.3056747 -0.1093680 -497.4150427 0.00 <------
CONF6 -34.1587465 0.76 -497.3049670 -0.1083824 -497.4133494 1.06
CONF7 -34.1578065 1.35 -497.2983644 -0.1105868 -497.4089512 3.82
CONF8 -34.1571241 1.78 -497.3029570 -0.1088296 -497.4117866 2.04
CONF9 -34.1570372 1.83 -497.3008248 -0.1088991 -497.4097239 3.34
CONF10 -34.1563217 2.28 -497.3038986 -0.1066580 -497.4105566 2.82
CONF11 -34.1559251 2.53 -497.3008250 -0.1096093 -497.4104343 2.89
CONF14 -34.1537285 3.91 -497.3022176 -0.1071149 -497.4093325 3.58
CONF15 -34.1529637 4.39 -497.3009381 -0.1099465 -497.4108846 2.61
--------------------------------------------------
Conformers considered further
--------------------------------------------------
Below the g_thr(1) threshold of 3.5 kcal/mol.
CONF1, CONF2, CONF3, CONF4, CONF5, CONF6, CONF8, CONF9, CONF10, CONF11, CONF15
--------------------------------------------------
Calculating prescreening G_mRRHO with implicit solvation!
The prescreening G_mRRHO calculation is now performed for:
CONF1, CONF2, CONF3, CONF4, CONF5, CONF6, CONF8, CONF9, CONF10, CONF11, CONF15
Constructed folders!
Starting 11 G_RRHO calculations.
Running GFN2-xTB mRRHO in CONF1/rrho_part1
Running GFN2-xTB mRRHO in CONF2/rrho_part1
Running GFN2-xTB mRRHO in CONF3/rrho_part1
Running GFN2-xTB mRRHO in CONF4/rrho_part1
Running GFN2-xTB mRRHO in CONF5/rrho_part1
Running GFN2-xTB mRRHO in CONF6/rrho_part1
Running GFN2-xTB mRRHO in CONF8/rrho_part1
Running GFN2-xTB mRRHO in CONF9/rrho_part1
Running GFN2-xTB mRRHO in CONF10/rrho_part1
Running GFN2-xTB mRRHO in CONF11/rrho_part1
Running GFN2-xTB mRRHO in CONF15/rrho_part1
Tasks completed!
The prescreening G_mRRHO calculation @ c1 was successful for CONF1/rrho_part1: 0.18287159
The prescreening G_mRRHO calculation @ c1 was successful for CONF2/rrho_part1: 0.18311981
The prescreening G_mRRHO calculation @ c1 was successful for CONF3/rrho_part1: 0.18287068
The prescreening G_mRRHO calculation @ c1 was successful for CONF4/rrho_part1: 0.18270975
The prescreening G_mRRHO calculation @ c1 was successful for CONF5/rrho_part1: 0.18272101
The prescreening G_mRRHO calculation @ c1 was successful for CONF6/rrho_part1: 0.18277331
The prescreening G_mRRHO calculation @ c1 was successful for CONF8/rrho_part1: 0.18239977
The prescreening G_mRRHO calculation @ c1 was successful for CONF9/rrho_part1: 0.18270475
The prescreening G_mRRHO calculation @ c1 was successful for CONF10/rrho_part1: 0.18264350
The prescreening G_mRRHO calculation @ c1 was successful for CONF11/rrho_part1: 0.18284194
The prescreening G_mRRHO calculation @ c1 was successful for CONF15/rrho_part1: 0.18323466
--------------------------------------------------
* Gibbs free energies of part1 *
--------------------------------------------------
CONF# G(GFNn-xTB) ΔG(GFNn-xTB) E [Eh] Gsolv [Eh] GmRRHO [Eh] Gtot ΔGtot
[a.u.] [kcal/mol] r2scan-3c COSMO-RS-normal GFN2 [Eh] [kcal/mol]
[r2scan-3c] [alpb]-bhess
CONF1 -33.9770832 0.00 -497.3021467 -0.1099952 0.1828716 -497.2292703 1.91
CONF2 -33.9763286 0.47 -497.3049956 -0.1092023 0.1831198 -497.2310781 0.78
CONF3 -33.9763824 0.44 -497.3064930 -0.1075368 0.1828707 -497.2311591 0.73
CONF4 -33.9763856 0.44 -497.3049058 -0.1082903 0.1827098 -497.2304863 1.15
CONF5 -33.9762040 0.55 -497.3056747 -0.1093680 0.1827210 -497.2323217 0.00 <------
CONF6 -33.9759732 0.70 -497.3049670 -0.1083824 0.1827733 -497.2305761 1.10
CONF8 -33.9747243 1.48 -497.3029570 -0.1088296 0.1823998 -497.2293868 1.84
CONF9 -33.9743324 1.73 -497.3008248 -0.1088991 0.1827047 -497.2270192 3.33
CONF10 -33.9736782 2.14 -497.3038986 -0.1066580 0.1826435 -497.2279131 2.77
CONF11 -33.9730831 2.51 -497.3008250 -0.1096093 0.1828419 -497.2275923 2.97
CONF15 -33.9697290 4.61 -497.3009381 -0.1099465 0.1832347 -497.2276500 2.93
Additional global 'fuzzy-threshold' based on the standard deviation of (G_mRRHO):
Std_dev(G_mRRHO) = 0.142 kcal/mol
Fuzzythreshold = 0.096 kcal/mol
Final sorting threshold G_thr(1) = 3.500 + 0.096 = 3.596 kcal/mol
Spearman correlation coefficient between (E + Solv) and (E + Solv + mRRHO) = 0.973
All relative (free) energies are below the initial G_thr(1) threshold of 3.5 kcal/mol.
All conformers are considered further.
Calculating Boltzmann averaged free energy of ensemble on input geometries (not DFT optimized)!
temperature /K: avE(T) /a.u. avGmRRHO(T) /a.u. avGsolv(T) /a.u. avG(T) /a.u.
----------------------------------------------------------------------------------------------------
298.15 -497.3054081 0.1827983 -0.1089068 -497.2315166 <<==part1==
----------------------------------------------------------------------------------------------------
Calculating unbiased GFNn-xTB energy
Constructed folders!
Starting 11 xTB - single-point calculations.
gfn2-xTB energy for CONF1/GFN_unbiased = -34.1764957
gfn2-xTB energy for CONF2/GFN_unbiased = -34.1762055
gfn2-xTB energy for CONF3/GFN_unbiased = -34.1760929
gfn2-xTB energy for CONF4/GFN_unbiased = -34.1757959
gfn2-xTB energy for CONF5/GFN_unbiased = -34.1758362
gfn2-xTB energy for CONF6/GFN_unbiased = -34.1754446
gfn2-xTB energy for CONF8/GFN_unbiased = -34.1740014
gfn2-xTB energy for CONF9/GFN_unbiased = -34.1737577
gfn2-xTB energy for CONF10/GFN_unbiased = -34.1732903
gfn2-xTB energy for CONF11/GFN_unbiased = -34.1730775
gfn2-xTB energy for CONF15/GFN_unbiased = -34.1709569
Tasks completed!
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>END of Part1<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
Ran part1 in 166.4199 seconds
----------------------------------------------------------------------------------------------------
CRE OPTIMIZATION - PART2
----------------------------------------------------------------------------------------------------
program: tm
functional for part2: r2scan-3c
basis set for part2: def2-mTZVPP
using the xTB-optimizer for optimization: on
using the new ensemble optimizer: on
optimize all conformers below this G_thr(opt,2) threshold: 2.5
Spearman threshold: 0.935
number of optimization iterations: 8
radsize: 10
optimization level in part2: lax
solvent: h2o
solvent model applied in the optimization: dcosmors
solvent model for Gsolv contribution: cosmors
temperature: 298.15
evalulate at different temperatures: on
temperature range: 273.15, 278.15, 283.15, 288.15, ...
Boltzmann sum threshold G_thr(2) for sorting in part2: 99.0
calculate mRRHO contribution: on
program for mRRHO contribution: xtb
GFN version for mRRHO and/or GBSA_Gsolv: gfn2
Apply constraint to input geometry during mRRHO calculation: on
Optimizing geometries at DFT level with implicit solvation!
The optimization is calculated for:
CONF1, CONF2, CONF3, CONF4, CONF5, CONF6, CONF8, CONF9, CONF10, CONF11, CONF15
Constructed folders!
Preparing 11 calculations.
Tasks completed!
************************Starting optimizations************************
Starting threshold is set to 2.5 + 60.0 % = 4.0 kcal/mol
Lower limit is set to G_thr(opt,2) = 2.5 kcal/mol
*******************************CYCLE 1********************************
Starting 11 optimizations.
Running optimization in CONF1/r2scan-3c
Running optimization in CONF2/r2scan-3c
Running optimization in CONF3/r2scan-3c
Running optimization in CONF4/r2scan-3c
Running optimization in CONF5/r2scan-3c
Running optimization in CONF6/r2scan-3c
Running optimization in CONF8/r2scan-3c
Running optimization in CONF9/r2scan-3c
Running optimization in CONF10/r2scan-3c
Running optimization in CONF11/r2scan-3c
Running optimization in CONF15/r2scan-3c
Tasks completed!
Constructed folders!
Starting 11 G_RRHO calculations.
Running GFN2-xTB mRRHO in r2scan-3c/rrho_crude
Running GFN2-xTB mRRHO in r2scan-3c/rrho_crude
Running GFN2-xTB mRRHO in r2scan-3c/rrho_crude
Running GFN2-xTB mRRHO in r2scan-3c/rrho_crude
Running GFN2-xTB mRRHO in r2scan-3c/rrho_crude
Running GFN2-xTB mRRHO in r2scan-3c/rrho_crude
Running GFN2-xTB mRRHO in r2scan-3c/rrho_crude
Running GFN2-xTB mRRHO in r2scan-3c/rrho_crude
Running GFN2-xTB mRRHO in r2scan-3c/rrho_crude
Running GFN2-xTB mRRHO in r2scan-3c/rrho_crude
Running GFN2-xTB mRRHO in r2scan-3c/rrho_crude
Tasks completed!
The G_mRRHO calculation on crudely optimized DFT geometry @ c1 was successful for CONF1/r2scan-3c/rrho_crude: 0.18253283
The G_mRRHO calculation on crudely optimized DFT geometry @ c1 was successful for CONF2/r2scan-3c/rrho_crude: 0.18217211
The G_mRRHO calculation on crudely optimized DFT geometry @ c1 was successful for CONF3/r2scan-3c/rrho_crude: 0.18223212
The G_mRRHO calculation on crudely optimized DFT geometry @ c1 was successful for CONF4/r2scan-3c/rrho_crude: 0.18258415
The G_mRRHO calculation on crudely optimized DFT geometry @ c1 was successful for CONF5/r2scan-3c/rrho_crude: 0.18245612
The G_mRRHO calculation on crudely optimized DFT geometry @ c1 was successful for CONF6/r2scan-3c/rrho_crude: 0.18170042
The G_mRRHO calculation on crudely optimized DFT geometry @ c1 was successful for CONF8/r2scan-3c/rrho_crude: 0.18260313
The G_mRRHO calculation on crudely optimized DFT geometry @ c1 was successful for CONF9/r2scan-3c/rrho_crude: 0.18272834
The G_mRRHO calculation on crudely optimized DFT geometry @ c1 was successful for CONF10/r2scan-3c/rrho_crude: 0.18229001
The G_mRRHO calculation on crudely optimized DFT geometry @ c1 was successful for CONF11/r2scan-3c/rrho_crude: 0.18150537
The G_mRRHO calculation on crudely optimized DFT geometry @ c1 was successful for CONF15/r2scan-3c/rrho_crude: 0.18100199
Max number of performed iterations: 8
Spearman rank evaluation is performed in the next cycle.
CONF1 initial ΔG = 2.13 kcal/mol and current ΔG = 2.59 kcal/mol. (not_converged)
CONF2 initial ΔG = 0.86 kcal/mol and current ΔG = 0.46 kcal/mol. (not_converged)
CONF3 initial ΔG = 0.97 kcal/mol and current ΔG = 1.47 kcal/mol. (not_converged)
CONF4 initial ΔG = 1.62 kcal/mol and current ΔG = 1.40 kcal/mol. (not_converged)
CONF5 initial ΔG = 0.00 kcal/mol and current ΔG = 0.42 kcal/mol. (not_converged)
CONF6 initial ΔG = 0.60 kcal/mol and current ΔG = 1.15 kcal/mol. (not_converged)
CONF8 initial ΔG = 2.26 kcal/mol and current ΔG = 2.31 kcal/mol. (not_converged)
CONF9 initial ΔG = 3.90 kcal/mol and current ΔG = 4.42 kcal/mol. (not_converged)
CONF10 initial ΔG = 2.86 kcal/mol and current ΔG = 2.92 kcal/mol. (not_converged)
CONF11 initial ΔG = 2.26 kcal/mol and current ΔG = 3.43 kcal/mol. (not_converged)
CONF15 initial ΔG = 0.23 kcal/mol and current ΔG = 0.00 kcal/mol. (not_converged)
CONF9 is above 4.0 kcal/mol and gradient norm (0.004056375026) is below 0.01.
CONF9 is above threshold, dont optimize further and remove conformer.
CYCLE 1 performed in 1310.1062 seconds
*******************************CYCLE 2********************************
Starting 10 optimizations.
Running optimization in CONF1/r2scan-3c
Running optimization in CONF2/r2scan-3c
Running optimization in CONF3/r2scan-3c
Running optimization in CONF4/r2scan-3c
Running optimization in CONF5/r2scan-3c
Running optimization in CONF6/r2scan-3c
Running optimization in CONF8/r2scan-3c
Running optimization in CONF10/r2scan-3c
Running optimization in CONF11/r2scan-3c
Running optimization in CONF15/r2scan-3c
Tasks completed!
Geometry optimization converged for: CONF3 within 12 cycles
Max number of performed iterations: 16
CONF1 previous ΔG = 2.59 kcal/mol and current ΔG = 2.54 kcal/mol. (not_converged)
CONF2 previous ΔG = 0.46 kcal/mol and current ΔG = 0.00 kcal/mol. (not_converged)
CONF3 previous ΔG = 1.47 kcal/mol and current ΔG = 1.92 kcal/mol. (converged)
CONF4 previous ΔG = 1.40 kcal/mol and current ΔG = 10.87 kcal/mol. (not_converged)
CONF5 previous ΔG = 0.42 kcal/mol and current ΔG = 0.99 kcal/mol. (not_converged)
CONF6 previous ΔG = 1.15 kcal/mol and current ΔG = 1.57 kcal/mol. (not_converged)
CONF8 previous ΔG = 2.31 kcal/mol and current ΔG = 1.85 kcal/mol. (not_converged)
CONF10 previous ΔG = 2.92 kcal/mol and current ΔG = 3.68 kcal/mol. (not_converged)
CONF11 previous ΔG = 3.43 kcal/mol and current ΔG = 3.29 kcal/mol. (not_converged)
CONF15 previous ΔG = 0.00 kcal/mol and current ΔG = 0.03 kcal/mol. (not_converged)
Spearman coeff. from 8 --> 11 = 0.9758
Spearman coeff. from 9 --> 12 = 0.9879
Spearman coeff. from 10 --> 13 = 0.7455
Spearman coeff. from 11 --> 14 = 1.0000
Evaluating Spearman coeff. from 12 --> 15 = 0.9515
Evaluating Spearman coeff. from 13 --> 16 = 0.8667
Final averaged Spearman correlation coefficient: 0.9091
CONF4 is above 4.0 kcal/mol but gradient norm (0.108293192291) is above 0.01 --> not sorted out!
CYCLE 2 performed in 980.4814 seconds
*******************************CYCLE 3********************************
Starting 9 optimizations.
Running optimization in CONF1/r2scan-3c
Running optimization in CONF2/r2scan-3c
Running optimization in CONF4/r2scan-3c
Running optimization in CONF5/r2scan-3c
Running optimization in CONF6/r2scan-3c
Running optimization in CONF8/r2scan-3c
Running optimization in CONF10/r2scan-3c
Running optimization in CONF11/r2scan-3c
Running optimization in CONF15/r2scan-3c
Tasks completed!
Geometry optimization converged for: CONF5 within 23 cycles
Geometry optimization converged for: CONF11 within 21 cycles
Max number of performed iterations: 24
CONF1 previous ΔG = 2.54 kcal/mol and current ΔG = 2.38 kcal/mol. (not_converged)
CONF2 previous ΔG = 0.00 kcal/mol and current ΔG = 0.00 kcal/mol. (not_converged)
CONF3 previous ΔG = 1.92 kcal/mol and current ΔG = 2.09 kcal/mol. (converged)
CONF4 previous ΔG = 10.87 kcal/mol and current ΔG = 0.07 kcal/mol. (not_converged)
CONF5 previous ΔG = 0.99 kcal/mol and current ΔG = 1.25 kcal/mol. (converged)
CONF6 previous ΔG = 1.57 kcal/mol and current ΔG = 1.51 kcal/mol. (not_converged)
CONF8 previous ΔG = 1.85 kcal/mol and current ΔG = 1.89 kcal/mol. (not_converged)
CONF10 previous ΔG = 3.68 kcal/mol and current ΔG = 3.36 kcal/mol. (not_converged)
CONF11 previous ΔG = 3.29 kcal/mol and current ΔG = 3.30 kcal/mol. (converged)
CONF15 previous ΔG = 0.03 kcal/mol and current ΔG = 0.22 kcal/mol. (not_converged)
Spearman coeff. from 16 --> 19 = 0.6606
Spearman coeff. from 17 --> 20 = 0.6000
Spearman coeff. from 18 --> 21 = 0.7455
Spearman coeff. from 19 --> 22 = 0.8182
Evaluating Spearman coeff. from 20 --> 23 = 0.7091
Evaluating Spearman coeff. from 21 --> 24 = 1.0000
Final averaged Spearman correlation coefficient: 0.8545
CYCLE 3 performed in 830.9565 seconds
*******************************CYCLE 4********************************
Starting 7 optimizations.
Running optimization in CONF1/r2scan-3c
Running optimization in CONF2/r2scan-3c
Running optimization in CONF4/r2scan-3c
Running optimization in CONF6/r2scan-3c
Running optimization in CONF8/r2scan-3c
Running optimization in CONF10/r2scan-3c
Running optimization in CONF15/r2scan-3c
Tasks completed!
Geometry optimization converged for: CONF8 within 26 cycles
Geometry optimization converged for: CONF15 within 25 cycles
Max number of performed iterations: 32
CONF1 previous ΔG = 2.38 kcal/mol and current ΔG = 1.84 kcal/mol. (not_converged)
CONF2 previous ΔG = 0.00 kcal/mol and current ΔG = 0.00 kcal/mol. (not_converged)
CONF3 previous ΔG = 2.09 kcal/mol and current ΔG = 2.11 kcal/mol. (converged)
CONF4 previous ΔG = 0.07 kcal/mol and current ΔG = 0.01 kcal/mol. (not_converged)
CONF5 previous ΔG = 1.25 kcal/mol and current ΔG = 1.26 kcal/mol. (converged)
CONF6 previous ΔG = 1.51 kcal/mol and current ΔG = 1.57 kcal/mol. (not_converged)
CONF8 previous ΔG = 1.89 kcal/mol and current ΔG = 1.91 kcal/mol. (converged)
CONF10 previous ΔG = 3.36 kcal/mol and current ΔG = 6.58 kcal/mol. (not_converged)
CONF11 previous ΔG = 3.30 kcal/mol and current ΔG = 3.32 kcal/mol. (converged)
CONF15 previous ΔG = 0.22 kcal/mol and current ΔG = 0.23 kcal/mol. (converged)
Spearman coeff. from 24 --> 27 = 0.9636
Spearman coeff. from 25 --> 28 = 0.9879
Spearman coeff. from 26 --> 29 = 0.9758
Spearman coeff. from 27 --> 30 = 0.8424
Evaluating Spearman coeff. from 28 --> 31 = 0.9515
Evaluating Spearman coeff. from 29 --> 32 = 0.9636
Final averaged Spearman correlation coefficient: 0.9576
PES is assumed to be parallel
Updated optimization threshold to: 3.50 kcal/mol
CONF10 is above 3.5 kcal/mol but gradient norm (0.09473608827) is above 0.01 --> not sorted out!
CYCLE 4 performed in 613.0740 seconds
*******************************CYCLE 5********************************
Starting 5 optimizations.
Running optimization in CONF1/r2scan-3c
Running optimization in CONF2/r2scan-3c
Running optimization in CONF4/r2scan-3c
Running optimization in CONF6/r2scan-3c
Running optimization in CONF10/r2scan-3c
Tasks completed!
Geometry optimization converged for: CONF2 within 34 cycles
Geometry optimization converged for: CONF6 within 39 cycles
Max number of performed iterations: 40
CONF1 previous ΔG = 1.84 kcal/mol and current ΔG = 7.79 kcal/mol. (not_converged)
CONF2 previous ΔG = 0.00 kcal/mol and current ΔG = 0.38 kcal/mol. (converged)
CONF3 previous ΔG = 2.11 kcal/mol and current ΔG = 2.53 kcal/mol. (converged)
CONF4 previous ΔG = 0.01 kcal/mol and current ΔG = 0.35 kcal/mol. (not_converged)
CONF5 previous ΔG = 1.26 kcal/mol and current ΔG = 1.68 kcal/mol. (converged)
CONF6 previous ΔG = 1.57 kcal/mol and current ΔG = 1.94 kcal/mol. (converged)
CONF8 previous ΔG = 1.91 kcal/mol and current ΔG = 2.33 kcal/mol. (converged)
CONF10 previous ΔG = 6.58 kcal/mol and current ΔG = 0.00 kcal/mol. (not_converged)
CONF11 previous ΔG = 3.32 kcal/mol and current ΔG = 3.74 kcal/mol. (converged)
CONF15 previous ΔG = 0.23 kcal/mol and current ΔG = 0.65 kcal/mol. (converged)
Spearman coeff. from 32 --> 35 = 0.7333
Spearman coeff. from 33 --> 36 = 0.9273
Spearman coeff. from 34 --> 37 = 0.8182
Spearman coeff. from 35 --> 38 = 1.0000
Evaluating Spearman coeff. from 36 --> 39 = 0.9879
Evaluating Spearman coeff. from 37 --> 40 = 0.8545
Final averaged Spearman correlation coefficient: 0.9212
CONF1 is above 3.5 kcal/mol but gradient norm (0.083474094636) is above 0.01 --> not sorted out!
CYCLE 5 performed in 403.3400 seconds
*******************************CYCLE 6********************************
Starting 3 optimizations.
Running optimization in CONF1/r2scan-3c
Running optimization in CONF4/r2scan-3c
Running optimization in CONF10/r2scan-3c
Tasks completed!
Geometry optimization converged for: CONF4 within 44 cycles
Max number of performed iterations: 48
CONF1 previous ΔG = 7.79 kcal/mol and current ΔG = 2.37 kcal/mol. (not_converged)
CONF2 previous ΔG = 0.38 kcal/mol and current ΔG = 1.25 kcal/mol. (converged)
CONF3 previous ΔG = 2.53 kcal/mol and current ΔG = 3.40 kcal/mol. (converged)
CONF4 previous ΔG = 0.35 kcal/mol and current ΔG = 1.19 kcal/mol. (converged)
CONF5 previous ΔG = 1.68 kcal/mol and current ΔG = 2.55 kcal/mol. (converged)
CONF6 previous ΔG = 1.94 kcal/mol and current ΔG = 2.80 kcal/mol. (converged)
CONF8 previous ΔG = 2.33 kcal/mol and current ΔG = 3.20 kcal/mol. (converged)
CONF10 previous ΔG = 0.00 kcal/mol and current ΔG = 0.00 kcal/mol. (not_converged)
CONF11 previous ΔG = 3.74 kcal/mol and current ΔG = 4.61 kcal/mol. (converged)
CONF15 previous ΔG = 0.65 kcal/mol and current ΔG = 1.52 kcal/mol. (converged)
Spearman coeff. from 40 --> 43 = 0.8788
Spearman coeff. from 41 --> 44 = 0.6242
Spearman coeff. from 42 --> 45 = 0.9273
Spearman coeff. from 43 --> 46 = 1.0000
Evaluating Spearman coeff. from 44 --> 47 = 0.6485
Evaluating Spearman coeff. from 45 --> 48 = 0.9879
Final averaged Spearman correlation coefficient: 0.8182
CYCLE 6 performed in 296.2324 seconds
*******************************CYCLE 7********************************
Starting 2 optimizations.
Running optimization in CONF1/r2scan-3c
Running optimization in CONF10/r2scan-3c
Tasks completed!
Max number of performed iterations: 56
CONF1 previous ΔG = 2.37 kcal/mol and current ΔG = 2.60 kcal/mol. (not_converged)
CONF2 previous ΔG = 1.25 kcal/mol and current ΔG = 1.66 kcal/mol. (converged)
CONF3 previous ΔG = 3.40 kcal/mol and current ΔG = 3.81 kcal/mol. (converged)
CONF4 previous ΔG = 1.19 kcal/mol and current ΔG = 1.61 kcal/mol. (converged)
CONF5 previous ΔG = 2.55 kcal/mol and current ΔG = 2.97 kcal/mol. (converged)
CONF6 previous ΔG = 2.80 kcal/mol and current ΔG = 3.22 kcal/mol. (converged)
CONF8 previous ΔG = 3.20 kcal/mol and current ΔG = 3.61 kcal/mol. (converged)
CONF10 previous ΔG = 0.00 kcal/mol and current ΔG = 0.00 kcal/mol. (not_converged)
CONF11 previous ΔG = 4.61 kcal/mol and current ΔG = 5.02 kcal/mol. (converged)
CONF15 previous ΔG = 1.52 kcal/mol and current ΔG = 1.94 kcal/mol. (converged)
Spearman coeff. from 48 --> 51 = 1.0000
Spearman coeff. from 49 --> 52 = 1.0000
Spearman coeff. from 50 --> 53 = 1.0000
Spearman coeff. from 51 --> 54 = 1.0000
Evaluating Spearman coeff. from 52 --> 55 = 1.0000
Evaluating Spearman coeff. from 53 --> 56 = 1.0000
Final averaged Spearman correlation coefficient: 1.0000
PES is assumed to be parallel
Updated optimization threshold to: 3.00 kcal/mol
CYCLE 7 performed in 252.6446 seconds
*******************************CYCLE 8********************************
Starting 2 optimizations.
Running optimization in CONF1/r2scan-3c
Running optimization in CONF10/r2scan-3c
Tasks completed!
Max number of performed iterations: 64
CONF1 previous ΔG = 2.60 kcal/mol and current ΔG = 2.71 kcal/mol. (not_converged)
CONF2 previous ΔG = 1.66 kcal/mol and current ΔG = 1.87 kcal/mol. (converged)
CONF3 previous ΔG = 3.81 kcal/mol and current ΔG = 4.02 kcal/mol. (converged)
CONF4 previous ΔG = 1.61 kcal/mol and current ΔG = 1.81 kcal/mol. (converged)
CONF5 previous ΔG = 2.97 kcal/mol and current ΔG = 3.17 kcal/mol. (converged)
CONF6 previous ΔG = 3.22 kcal/mol and current ΔG = 3.42 kcal/mol. (converged)
CONF8 previous ΔG = 3.61 kcal/mol and current ΔG = 3.82 kcal/mol. (converged)
CONF10 previous ΔG = 0.00 kcal/mol and current ΔG = 0.00 kcal/mol. (not_converged)
CONF11 previous ΔG = 5.02 kcal/mol and current ΔG = 5.23 kcal/mol. (converged)
CONF15 previous ΔG = 1.94 kcal/mol and current ΔG = 2.14 kcal/mol. (converged)
Spearman coeff. from 56 --> 59 = 1.0000
Spearman coeff. from 57 --> 60 = 1.0000
Spearman coeff. from 58 --> 61 = 1.0000
Spearman coeff. from 59 --> 62 = 1.0000
Evaluating Spearman coeff. from 60 --> 63 = 1.0000
Evaluating Spearman coeff. from 61 --> 64 = 1.0000
Final averaged Spearman correlation coefficient: 1.0000
PES is assumed to be parallel
Updated optimization threshold to: 2.50 kcal/mol
CONF1 is above 2.5 kcal/mol and gradient norm (0.001262363132) is below 0.01.
CONF1 is removed because of the lowered threshold!
CONF1 is above threshold, dont optimize further and remove conformer.
CYCLE 8 performed in 251.6678 seconds
*******************************CYCLE 9********************************
Starting 1 optimizations.
Running optimization in CONF10/r2scan-3c
Tasks completed!
Max number of performed iterations: 72
CONF2 previous ΔG = 1.87 kcal/mol and current ΔG = 1.84 kcal/mol. (converged)
CONF3 previous ΔG = 4.02 kcal/mol and current ΔG = 3.99 kcal/mol. (converged)
CONF4 previous ΔG = 1.81 kcal/mol and current ΔG = 1.78 kcal/mol. (converged)
CONF5 previous ΔG = 3.17 kcal/mol and current ΔG = 3.14 kcal/mol. (converged)
CONF6 previous ΔG = 3.42 kcal/mol and current ΔG = 3.39 kcal/mol. (converged)
CONF8 previous ΔG = 3.82 kcal/mol and current ΔG = 3.79 kcal/mol. (converged)
CONF10 previous ΔG = 0.00 kcal/mol and current ΔG = 0.00 kcal/mol. (not_converged)
CONF11 previous ΔG = 5.23 kcal/mol and current ΔG = 5.20 kcal/mol. (converged)
CONF15 previous ΔG = 2.14 kcal/mol and current ΔG = 2.11 kcal/mol. (converged)
Spearman coeff. from 64 --> 67 = 1.0000
Spearman coeff. from 65 --> 68 = 1.0000
Spearman coeff. from 66 --> 69 = 1.0000
Spearman coeff. from 67 --> 70 = 1.0000
Evaluating Spearman coeff. from 68 --> 71 = 1.0000
Evaluating Spearman coeff. from 69 --> 72 = 1.0000
Final averaged Spearman correlation coefficient: 1.0000
PES is assumed to be parallel
Current optimization threshold: 2.50 kcal/mol
CYCLE 9 performed in 202.2149 seconds
*******************************CYCLE 10*******************************
Starting 1 optimizations.
Running optimization in CONF10/r2scan-3c
Tasks completed!
Geometry optimization converged for: CONF10 within 80 cycles
***********************Finished optimizations!************************
Timings:
Cycle: [s]
1 1310.11
2 980.48
3 830.96
4 613.07
5 403.34
6 296.23
7 252.64
8 251.67
9 202.21
10 200.34
sum: 5341.06
CONVERGED optimizations for the following remaining conformers:
Converged optimization for CONF2 after 34 cycles: -497.4508410
Converged optimization for CONF3 after 12 cycles: -497.4474711
Converged optimization for CONF4 after 44 cycles: -497.4513419
Converged optimization for CONF5 after 23 cycles: -497.4490457
Converged optimization for CONF6 after 39 cycles: -497.4478893
Converged optimization for CONF8 after 26 cycles: -497.4481610
Converged optimization for CONF10 after 80 cycles: -497.4538409
Converged optimization for CONF11 after 21 cycles: -497.4448166
Converged optimization for CONF15 after 25 cycles: -497.4492319
Calculating single-point energies and solvation contribution (G_solv)!
The low level gsolv calculation is now calculated for:
Constructed folders!
CONF2, CONF3, CONF4, CONF5, CONF6, CONF8, CONF10, CONF11, CONF15
Starting 9 COSMO-RS-Gsolv calculations.
Running COSMO-RS calculation in CONF2/r2scan-3c/COSMO
Running COSMO-RS calculation in CONF3/r2scan-3c/COSMO
Running COSMO-RS calculation in CONF4/r2scan-3c/COSMO
Running COSMO-RS calculation in CONF5/r2scan-3c/COSMO
Running COSMO-RS calculation in CONF6/r2scan-3c/COSMO
Running COSMO-RS calculation in CONF8/r2scan-3c/COSMO
Running COSMO-RS calculation in CONF10/r2scan-3c/COSMO
Running COSMO-RS calculation in CONF11/r2scan-3c/COSMO
Running COSMO-RS calculation in CONF15/r2scan-3c/COSMO
Tasks completed!
lowlevel COSMO-RS calculation was successful for CONF2/r2scan-3c/COSMO: -0.13589836
lowlevel COSMO-RS calculation was successful for CONF3/r2scan-3c/COSMO: -0.12865185
lowlevel COSMO-RS calculation was successful for CONF4/r2scan-3c/COSMO: -0.13533997
lowlevel COSMO-RS calculation was successful for CONF5/r2scan-3c/COSMO: -0.12940253
lowlevel COSMO-RS calculation was successful for CONF6/r2scan-3c/COSMO: -0.12980575
lowlevel COSMO-RS calculation was successful for CONF8/r2scan-3c/COSMO: -0.12959608
lowlevel COSMO-RS calculation was successful for CONF10/r2scan-3c/COSMO: -0.15938290
lowlevel COSMO-RS calculation was successful for CONF11/r2scan-3c/COSMO: -0.13131124
lowlevel COSMO-RS calculation was successful for CONF15/r2scan-3c/COSMO: -0.13806979
Calculating lowlevel G_mRRHO with implicit solvation on DFT geometry!
The lowlevel G_mRRHO calculation is now performed for:
CONF2, CONF3, CONF4, CONF5, CONF6, CONF8, CONF10, CONF11, CONF15
Constructed folders!
Starting 9 G_RRHO calculations.
Running GFN2-xTB mRRHO in CONF2/rrho_part2
Running GFN2-xTB mRRHO in CONF3/rrho_part2
Running GFN2-xTB mRRHO in CONF4/rrho_part2
Running GFN2-xTB mRRHO in CONF5/rrho_part2
Running GFN2-xTB mRRHO in CONF6/rrho_part2
Running GFN2-xTB mRRHO in CONF8/rrho_part2
Running GFN2-xTB mRRHO in CONF10/rrho_part2
Running GFN2-xTB mRRHO in CONF11/rrho_part2
Running GFN2-xTB mRRHO in CONF15/rrho_part2
Tasks completed!
The lowlevel G_mRRHO calculation @ c1 was successful for CONF2/rrho_part2: 0.18028469
The lowlevel G_mRRHO calculation @ c1 was successful for CONF3/rrho_part2: 0.18207391
The lowlevel G_mRRHO calculation @ c1 was successful for CONF4/rrho_part2: 0.18117449
The lowlevel G_mRRHO calculation @ c1 was successful for CONF5/rrho_part2: 0.18231888
The lowlevel G_mRRHO calculation @ c1 was successful for CONF6/rrho_part2: 0.18172189
The lowlevel G_mRRHO calculation @ c1 was successful for CONF8/rrho_part2: 0.18218769
The lowlevel G_mRRHO calculation @ c1 was successful for CONF10/rrho_part2: 0.17889859
The lowlevel G_mRRHO calculation @ c1 was successful for CONF11/rrho_part2: 0.18153296
The lowlevel G_mRRHO calculation @ c1 was successful for CONF15/rrho_part2: 0.18070768
--------------------------------------------------
* Gibbs free energies of part2 *
--------------------------------------------------
CONF# E(GFNn-xTB) ΔE(GFNn-xTB) E [Eh] Gsolv [Eh] GmRRHO [Eh] Gtot ΔGtot Boltzmannweight
[a.u.] [kcal/mol] r2scan-3c COSMO-RS-normal GFN2 [Eh] [kcal/mol] % at 298.15 K
[r2scan-3c] [alpb]-bhess
CONF2 -34.1594484 0.32 -497.2837810 -0.1358984 0.1802847 -497.2393947 0.17 21.10
CONF3 -34.1592530 0.44 -497.2915335 -0.1286518 0.1820739 -497.2381114 0.98 5.42
CONF4 -34.1590954 0.54 -497.2853431 -0.1353400 0.1811745 -497.2395086 0.10 23.80
CONF5 -34.1589250 0.65 -497.2917403 -0.1294025 0.1823189 -497.2388239 0.53 11.53
CONF6 -34.1587465 0.76 -497.2896963 -0.1298058 0.1817219 -497.2377802 1.19 3.82
CONF8 -34.1571241 1.78 -497.2905928 -0.1295961 0.1821877 -497.2380012 1.05 4.82
CONF10 -34.1563217 2.28 -497.2591855 -0.1593829 0.1788986 -497.2396698 0.00 28.23 <------
CONF11 -34.1559251 2.53 -497.2848139 -0.1313112 0.1815330 -497.2345922 3.19 0.13
CONF15 -34.1529637 4.39 -497.2792896 -0.1380698 0.1807077 -497.2366518 1.89 1.15
Calculating ALPB_Gsolv values for evaluation of the std. dev. of Gsolv.
Constructed folders!
Starting 9 ALPB-Gsolv calculations
Running ALPB_GSOLV calculation in 3-part0-2/CONF2/alpb_gsolv
Running ALPB_GSOLV calculation in 3-part0-2/CONF3/alpb_gsolv
Running ALPB_GSOLV calculation in 3-part0-2/CONF4/alpb_gsolv
Running ALPB_GSOLV calculation in 3-part0-2/CONF5/alpb_gsolv
Running ALPB_GSOLV calculation in 3-part0-2/CONF6/alpb_gsolv
Running ALPB_GSOLV calculation in 3-part0-2/CONF8/alpb_gsolv
Running ALPB_GSOLV calculation in 3-part0-2/CONF10/alpb_gsolv
Running ALPB_GSOLV calculation in 3-part0-2/CONF11/alpb_gsolv
Running ALPB_GSOLV calculation in 3-part0-2/CONF15/alpb_gsolv
Tasks completed!
ALPB_GSOLV calculation was successful for CONF2/alpb_gsolv: -0.14572423
ALPB_GSOLV calculation was successful for CONF3/alpb_gsolv: -0.14136373
ALPB_GSOLV calculation was successful for CONF4/alpb_gsolv: -0.14534319
ALPB_GSOLV calculation was successful for CONF5/alpb_gsolv: -0.14108828
ALPB_GSOLV calculation was successful for CONF6/alpb_gsolv: -0.14215086
ALPB_GSOLV calculation was successful for CONF8/alpb_gsolv: -0.14150861
ALPB_GSOLV calculation was successful for CONF10/alpb_gsolv: -0.16262359
ALPB_GSOLV calculation was successful for CONF11/alpb_gsolv: -0.14230853
ALPB_GSOLV calculation was successful for CONF15/alpb_gsolv: -0.14881714
SD of solvation models (all units in kcal/mol):
CONFX ΔG(COSMO-RS) ΔG(DCOSMO-RS_gsolv) ΔG(ALPB_gsolv) SD(COSMO-RS 40%, DCOSMO-RS_gsolv 40%, ALPB_gsolv 20%)
----------------------------------------------------------------------------------------------------
CONF2 14.74 17.32 10.60 3.01
CONF3 19.28 24.30 13.34 4.97
CONF4 15.09 17.98 10.84 3.21
CONF5 18.81 23.44 13.51 4.51
CONF6 18.56 22.88 12.85 4.53
CONF8 18.69 23.27 13.25 4.54
CONF10 0.00 0.00 0.00 0.00
CONF11 17.62 21.74 12.75 4.08
CONF15 13.37 15.51 8.66 3.06
----------------------------------------------------------------------------------------------------
Calculating Boltzmann averaged free energy of ensemble!
temperature /K: avE(T) /a.u. avGmRRHO(T) /a.u. avGsolv(T) /a.u. avG(T) /a.u.
----------------------------------------------------------------------------------------------------
273.15 -497.2736863 0.1842434 -0.1489372 -497.2383801
278.15 -497.2749007 0.1835285 -0.1471130 -497.2384852
283.15 -497.2760521 0.1828067 -0.1453716 -497.2386171
288.15 -497.2771316 0.1820765 -0.1437255 -497.2387805
293.15 -497.2781302 0.1813377 -0.1421818 -497.2389743
298.15 -497.2790497 0.1805897 -0.1407374 -497.2391974 <<==part2==
303.15 -497.2798874 0.1798315 -0.1393937 -497.2394496
308.15 -497.2806529 0.1790640 -0.1381406 -497.2397295
313.15 -497.2813425 0.1782861 -0.1369800 -497.2400363
318.15 -497.2819636 0.1774979 -0.1359037 -497.2403694
323.15 -497.2825199 0.1767001 -0.1349073 -497.2407270
328.15 -497.2830226 0.1758934 -0.1339792 -497.2411084
333.15 -497.2834731 0.1750769 -0.1331172 -497.2415134
338.15 -497.2838754 0.1742509 -0.1323164 -497.2419409
343.15 -497.2842354 0.1734163 -0.1315708 -497.2423900
348.15 -497.2845604 0.1725735 -0.1308732 -497.2428601
353.15 -497.2848497 0.1717219 -0.1302228 -497.2433506
358.15 -497.2851101 0.1708621 -0.1296129 -497.2438610
363.15 -497.2853448 0.1699946 -0.1290401 -497.2443904
368.15 -497.2855549 0.1691186 -0.1285027 -497.2449389
373.15 -497.2857417 0.1682355 -0.1279985 -497.2455047
----------------------------------------------------------------------------------------------------
--------------------------------------------------
Conformers considered further
--------------------------------------------------
Conformers that are below the Boltzmann threshold G_thr(2) of 99.0%:
CONF10, CONF4, CONF2, CONF5, CONF3, CONF8, CONF6, CONF15
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>END of Part2<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
Ran part2 in 5486.1036 seconds
Part : #conf time
--------------------------------------------------
Input : 22 -
Part0_all : 13 25.32s
Part1_initial_sort : 11 -
Part1_all : 11 166.42s
Part2_opt : 9 -
Part2_all : 8 5486.10s
--------------------------------------------------
All parts : 5677.84s
CENSO all done!
$CENSO global configuration file: .censorc
$VERSION:1.0.3
ORCA: /home/$USER/orca_4_2_1_linux_x86-64_openmpi216
ORCA version: 4.2.1
GFN-xTB: /home/$USER/bin/xtb
CREST: /home/$USER/bin/crest
mpshift: mpshift
escf: escf
#COSMO-RS
ctd = BP_TZVPD_FINE_C30_1601.ctd cdir = "/home/$USER/COSMOlogic/COSMOthermX19/COSMOtherm/CTDATA-FILES" ldir = "/home/bohle/COSMOlogic/COSMOthermX19/COSMOtherm/CTDATA-FILES"
cosmothermversion: 19
$ENDPROGRAMS
$CRE SORTING SETTINGS:
$GENERAL SETTINGS:
nconf: all # ['all', 'number e.g. 10 up to all conformers']
charge: 1 # ['number e.g. 0']
unpaired: 0 # ['number e.g. 0']
solvent: h2o # ['gas', 'acetone', 'chcl3', 'acetonitrile', 'ch2cl2', 'dmso', 'h2o', 'methanol', 'thf', '...']
prog_rrho: xtb # ['xtb', 'prog']
temperature: 298.15 # ['temperature in K e.g. 298.15']
trange: [273.15, 378.15, 5] # ['temperature range [start, end, step]']
multitemp: on # ['on', 'off']
evaluate_rrho: on # ['on', 'off']
consider_sym: off # ['on', 'off']
bhess: on # ['on', 'off']
imagthr: automatic # ['automatic or e.g., -100 # in cm-1']
sthr: automatic # ['automatic or e.g., 50 # in cm-1']
scale: automatic # ['automatic or e.g., 1.0 ']
rmsdbias: off # ['on', 'off']
sm_rrho: alpb # ['alpb', 'gbsa']
check: on # ['on', 'off']
prog: tm # ['tm', 'orca']
func: r2scan-3c # ['pbe', 'b97-d', 'pbeh-3c', 'tpss', 'b97-d3', 'r2scan-3c', 'b97-3c']
basis: automatic # ['automatic', 'def2-mSVP', 'def2-mTZVP', 'def2-mTZVP', 'def2-TZVP', '...']
maxthreads: 4 # ['number of threads e.g. 2']
omp: 2 # ['number cores per thread e.g. 4']
cosmorsparam: automatic # ['automatic', '12-fine', '12-normal', '13-fine', '13-normal', '14-fine', '...']
$PART0 - CHEAP-PRESCREENING - SETTINGS:
part0: on # ['on', 'off']
func0: b97-d # ['pbeh-3c', 'b97-3c', 'b97-d3', 'pbe', 'r2scan-3c', 'tpss', 'b97-d']
basis0: def2-SV(P) # ['automatic', 'def2-mSVP', 'def2-mTZVP', 'def2-mTZVP', 'def2-TZVP', '...']
part0_gfnv: gfn2 # ['gfn1', 'gfn2', 'gfnff']
part0_threshold: 4.0 # ['number e.g. 4.0']
$PART1 - PRESCREENING - SETTINGS:
# func and basis is set under GENERAL SETTINGS
part1: on # ['on', 'off']
smgsolv1: cosmors # ['alpb_gsolv', 'dcosmors', 'cosmo', 'smd', 'cosmors-fine', 'cpcm', 'gbsa_gsolv', '...']
part1_gfnv: gfn2 # ['gfn1', 'gfn2', 'gfnff']
part1_threshold: 3.5 # ['number e.g. 5.0']
$PART2 - OPTIMIZATION - SETTINGS:
# func and basis is set under GENERAL SETTINGS
part2: on # ['on', 'off']
opt_limit: 2.5 # ['number e.g. 4.0']
sm2: dcosmors # ['cosmo', 'cpcm', 'default', 'smd', 'dcosmors']
smgsolv2: cosmors # ['cosmors-fine', 'gbsa_gsolv', 'cosmo', 'cpcm', 'smd_gsolv', 'alpb_gsolv', 'smd', '...']
part2_gfnv: gfn2 # ['gfn1', 'gfn2', 'gfnff']
ancopt: on # ['on']
hlow: 0.01 # ['lowest force constant in ANC generation, e.g. 0.01']
opt_spearman: on # ['on', 'off']
part2_threshold: 99 # ['Boltzmann sum threshold in %. e.g. 95 (between 1 and 100)']
optlevel2: automatic # ['crude', 'sloppy', 'loose', 'lax', 'normal', 'tight', 'vtight', 'extreme', '...']
optcycles: 8 # ['number e.g. 5 or 10']
spearmanthr: -4.0 # ['value between -1 and 1, if outside set automatically']
radsize: 10 # ['number e.g. 8 or 10']
crestcheck: off # ['on', 'off']
$PART3 - REFINEMENT - SETTINGS:
part3: off # ['on', 'off']
prog3: prog # ['tm', 'orca', 'prog']
func3: pw6b95 # ['dsd-blyp', 'pw6b95', 'b97-d3', 'r2scan-3c', 'pbe0', 'wb97x']
basis3: def2-TZVPD # ['SVP', 'SV(P)', 'TZVP', 'TZVPP', 'QZVP', 'QZVPP', 'def2-SV(P)', 'def2-mSVP', '...']
smgsolv3: cosmors # ['alpb_gsolv', 'dcosmors', 'cosmo', 'smd', 'cosmors-fine', 'cpcm', 'gbsa_gsolv', '...']
part3_gfnv: gfn2 # ['gfn1', 'gfn2', 'gfnff']
part3_threshold: 99 # ['Boltzmann sum threshold in %. e.g. 95 (between 1 and 100)']
$NMR PROPERTY SETTINGS:
$PART4 SETTINGS:
part4: off # ['on', 'off']
couplings: on # ['on', 'off']
progJ: prog # ['tm', 'orca', 'adf', 'prog']
funcJ: pbe0 # ['tpss', 'pbe0', 'pbeh-3c']
basisJ: def2-TZVP # ['SVP', 'SV(P)', 'TZVP', 'TZVPP', 'QZVP', 'QZVPP', 'def2-SV(P)', 'def2-mSVP', '...']
sm4J: default # ['dcosmors', 'smd', 'cosmo', 'cpcm']
shieldings: on # ['on', 'off']
progS: prog # ['tm', 'orca', 'adf', 'prog']
funcS: pbe0 # ['dsd-blyp', 'pbeh-3c', 'tpss', 'pbe0', 'kt2']
basisS: def2-TZVP # ['SVP', 'SV(P)', 'TZVP', 'TZVPP', 'QZVP', 'QZVPP', 'def2-SV(P)', 'def2-mSVP', '...']
sm4S: default # ['dcosmors', 'smd', 'cosmo', 'cpcm']
reference_1H: TMS # ['TMS']
reference_13C: TMS # ['TMS']
reference_19F: CFCl3 # ['CFCl3']
reference_29Si: TMS # ['TMS']
reference_31P: TMP # ['TMP', 'PH3']
1H_active: on # ['on', 'off']
13C_active: on # ['on', 'off']
19F_active: off # ['on', 'off']
29Si_active: off # ['on', 'off']
31P_active: off # ['on', 'off']
resonance_frequency: 300.0 # ['MHz number of your experimental spectrometer setup']
$OPTICAL ROTATION PROPERTY SETTINGS:
$PART5 SETTINGS:
optical_rotation: off # ['on', 'off']
funcOR: pbe # ['functional for opt_rot e.g. pbe']
funcOR_SCF: r2scan-3c # ['functional for SCF in opt_rot e.g. r2scan-3c']
basisOR: def2-SVPD # ['basis set for opt_rot e.g. def2-SVPD']
frequency_optical_rot: [589.0] # ['list of freq in nm to evaluate opt rot at e.g. [589, 700]']
$END CENSORC
25
-34.15995484
O -2.7404108553 -0.9210263756 0.0505546155
O -0.6532148483 -1.7303331963 0.1381884568
N -2.1811530948 1.4662136641 -0.3280604715
N 1.9999042791 -1.6115147219 -0.1737452561
C 1.2832974514 1.7494376339 0.2478643443
C 0.0382242755 1.0547713107 0.8044626435
C 2.1972182535 0.8461961224 -0.5852172042
C -0.9624505804 0.6276788621 -0.2713633850
C 2.7304045776 -0.3664138808 0.1827513585
C -1.5037598584 -0.8390454546 0.0048901917
H 1.8561477225 2.1402514306 1.0892838382
H 0.9852377848 2.6009114549 -0.3642611073
H -0.4518270956 1.7282098745 1.5089809935
H 0.3322545004 0.1775252924 1.3825123935
H 1.6820235078 0.5059218506 -1.4832357051
H 3.0380251642 1.4546200515 -0.9165284484
H -0.4868586610 0.6089411942 -1.2530945560
H 2.6388482788 -0.2021893439 1.2562535001
H 3.7853986884 -0.5188774904 -0.0473087348
H -2.2380899515 2.1426216511 0.4407329422
H -2.3218532286 1.9466721688 -1.2205963738
H 2.3394829642 -2.3992859458 0.3882351555
H 0.9350292280 -1.5547588441 -0.0165809300
H 2.1475890354 -1.8368760327 -1.1636223077
H -2.9328940343 0.6971914121 -0.1921053926
25
-34.15944839
O -2.5910945174 -0.7526707388 0.4737473250
O -0.5258609320 -1.6055473558 0.4259946366
N -2.1883047577 1.2429283468 -0.9276187078
N 2.0221224751 -1.5482527990 -0.3635876013
C 1.0959612422 0.9269941773 1.0928268792
C -0.1118183900 1.5287127427 0.3646185610
C 2.3883955950 0.8232150730 0.2771806877
C -0.9137052232 0.5859776609 -0.5447048684
C 2.3984857923 -0.1999516224 -0.8542391926
C -1.3796771114 -0.7342464594 0.2052799197
H 0.8202702309 -0.0346561349 1.5230052762
H 1.3150554091 1.5881707649 1.9329336393
H 0.2252898792 2.3837647705 -0.2251981715
H -0.7970460540 1.8894152433 1.1356879771
H 2.6174364896 1.7989347868 -0.1517789136
H 3.1942064704 0.5825472961 0.9724285437
H -0.3499369029 0.3059081761 -1.4335569624
H 3.4048136146 -0.2402683769 -1.2749539435
H 1.7122153210 0.0852818535 -1.6492945642
H -2.2438155060 2.2226460139 -0.6308218074
H -2.4094139539 1.1700691932 -1.9248068681
H 0.9927667520 -1.5675551657 -0.0428313977
H 2.1377830502 -2.2542373686 -1.0973459319
H 2.6054467969 -1.8083924261 0.4393088723
H -2.8796747565 0.6310313638 -0.3580585669
25
-34.15925304
O -2.6152400314 -1.0465052003 0.2378304729
O -0.5362082855 -1.4663149505 -0.4593671015
N -2.4557715395 1.4039918868 0.4362491058
N 2.1447268012 -1.5911295291 -0.0908488427
C 1.1849792140 1.1291603967 -0.7123125066
C 0.0549239500 1.3190958463 0.3109988160
C 2.5516538580 0.8614163999 -0.0796419105
C -1.2770304521 0.8481909298 -0.2699298296
C 2.6278492228 -0.4408272994 0.7143702153
C -1.4798499370 -0.7275247362 -0.1594413730
H 1.2638776944 2.0288103522 -1.3231621409
H 0.9216680773 0.3153070715 -1.3864974308
H -0.0132519646 2.3752873127 0.5749134480
H 0.2604586805 0.7576942571 1.2223482952
H 3.2969117377 0.8423750312 -0.8755852689
H 2.8115908685 1.6810094994 0.5898815386
H -1.3353089850 1.1014685130 -1.3310936133
H 2.0240292821 -0.3842292575 1.6193674755
H 3.6638250279 -0.6160286136 1.0070988283
H -2.2160156909 1.7709567167 1.3631094761
H -2.9723151833 2.1102297821 -0.0929227069
H 2.6253531272 -1.6216026098 -0.9974699479
H 2.3064470721 -2.4761725884 0.4009650983
H 1.0998172314 -1.5111491960 -0.2664030290
H -3.0342449423 0.4895941432 0.5473101358
25
-34.15909539
O -2.5859531813 -0.8098009525 0.4685129327
O -0.4816245052 -1.5436026390 0.3102868940
N -2.3339104715 1.3007756781 -0.7836622820
N 2.0492564794 -1.5871472251 -0.5900906398
C 1.1052196056 0.9870949301 0.9271737021
C -0.2140772115 1.5925038037 0.4451868362
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O -3.5578446821 0.0350414384 0.6950996250
N -1.7249631955 1.6316108345 0.4298941943
N 4.8503432460 -0.2765578553 0.0049566510
C 1.1047501969 0.4501828237 -0.3379055216
C -0.1445140391 -0.2886936630 0.1459845288
C 2.3741940866 -0.2828979224 0.0965187068
C -1.4339016427 0.3793165613 -0.3028003047
C 3.6160850376 0.4539254738 -0.3951671902
C -2.6934727541 -0.5488189533 -0.0039847520
H 1.1202182595 1.4641232269 0.0631636060
H 1.0744507790 0.5160807326 -1.4261342120
H -0.1466884742 -0.3764861277 1.2347858649
H -0.1614173698 -1.3033571375 -0.2567289346
H 2.3826839006 -0.3550960319 1.1849100754
H 2.3458274825 -1.2937888279 -0.3120785959
H -1.4193517541 0.5529473168 -1.3796978179
H 3.6476836700 1.4575725004 0.0303995802
H 3.5908364898 0.5356651831 -1.4823627548
H -1.7888195298 2.4639789876 -0.1581990321
H -2.7206446817 1.3385249836 0.8116492773
H 5.6915565940 0.2174183391 -0.3259194480
H 4.8962264202 -0.3605243899 1.0314916029
H 4.8443782262 -1.2261178281 -0.3963638456
H -1.0847775954 1.7904079765 1.2125175138
25
-34.15096274
O -3.0664396656 -0.6811514259 0.4732552569
O -1.1830540829 -1.6357953168 -0.2743493731
N -2.5677177347 1.6455787239 -0.0357930901
N 3.4161836207 -1.4947231742 0.0043983586
C 1.0526738400 0.4198619079 -0.3271341828
C -0.1392962419 1.1756334823 0.2601668795
C 2.3301787116 0.6870764296 0.4694516416
C -1.4374925629 0.7826136622 -0.4432938226
C 3.5433351448 -0.0155439223 -0.1263696890
C -1.9232732343 -0.6849210780 -0.0466890927
H 1.1914397265 0.7321338619 -1.3635085567
H 0.7858921189 -0.6373779302 -0.3204311762
H 0.0218209785 2.2505182304 0.1468292069
H -0.2266241551 0.9455046686 1.3247226359
H 2.5278796928 1.7590277621 0.4727119199
H 2.1882724928 0.3782271446 1.5058219746
H -1.3025118280 0.8032883597 -1.5259809861
H 4.4479425383 0.3027435209 0.3921583620
H 3.6346463266 0.2349775607 -1.1836334244
H -3.0211573542 2.1410074345 -0.8045922540
H -3.2218629847 0.8371482423 0.3587042034
H 4.2253281871 -1.9726822174 -0.4155872948
H 3.3489651634 -1.7581308116 0.9983748528
H 2.5570336567 -1.8144640232 -0.4679619280
H -2.3203269015 2.3008181314 0.7098687755
25
-34.15085064
O -3.5353488917 0.0322108098 0.4084906022
O -2.4254579214 -1.9084093375 0.6284254091
N -1.7744403653 1.3652775888 -0.6438663864
N 4.1843308757 -0.1227935311 -1.0149931633
C 1.2054477125 0.3338345853 -0.2573250215
C -0.0723683835 -0.0922253390 0.4701395235
C 2.4067626747 0.2476116899 0.6871054133
C -1.3095998224 -0.0201188789 -0.4106994862
C 3.6989393857 0.7735207317 0.0732627710
C -2.5481677099 -0.7347193516 0.2919952398
H 1.1039179513 1.3593179418 -0.6150772671
H 1.3305507433 -0.3269971917 -1.1156830038
H -0.2323641779 0.5179203592 1.3619095074
H 0.0148258366 -1.1272987239 0.8068454593
H 2.1939049448 0.8432977651 1.5748900270
H 2.5356727482 -0.7824695024 1.0211816116
H -1.1430786561 -0.5391980852 -1.3555500184
H 4.4681954117 0.8303339300 0.8434799998
H 3.5410323285 1.7707403176 -0.3387001734
H -2.7959421798 1.2370421526 -0.2418926774
H -1.2663143192 2.0543977636 -0.0827359543
H 4.3101055621 -1.0795234870 -0.6518667702
H 3.4997443822 -0.1538144186 -1.7841531054
H 5.0842467659 0.2120203831 -1.3873716549
H -1.8037773550 1.6476905491 -1.6249441216
25
-34.15048917
O -1.9774584219 -0.8822136242 -1.3447844876
O -0.7353222350 -1.3040874260 0.4712779300
N -1.2018711229 0.8204001109 1.6759883927
N 1.9464051556 -1.6923491374 0.3496868798
C 0.8058411616 1.0462579377 -0.9468506072
C -0.4754178942 1.7785998054 -0.5275051890
C 1.8226970853 0.7789686777 0.1752315710
C -1.5019161161 0.9155320919 0.2220611780
C 2.6576744598 -0.4659344426 -0.1177787426
C -1.4255171488 -0.5796126398 -0.2987743324
H 1.2927227489 1.6467822241 -1.7161034319
H 0.5115436171 0.1136959367 -1.4299162738
H -0.9626535770 2.1244807715 -1.4395462399
H -0.2313854006 2.6631384020 0.0636669169
H 2.4836824282 1.6401220787 0.2631946203
H 1.3379895832 0.6415415675 1.1385387246
H -2.5044279955 1.3042479639 0.0511624497
H 3.6220420553 -0.4105315490 0.3870533340
H 2.8346807725 -0.5412209492 -1.1903941633
H -0.5537202797 1.5469435382 2.0029686770
H -2.0510266978 0.8448716653 2.2497725116
H 0.8939724574 -1.6086997720 0.2334441992
H 2.2630899289 -2.5235198565 -0.1606712473
H 2.1155048181 -1.8450780227 1.3513380594
H -0.7798223195 -0.1709536166 1.7101046448
25
-34.15043307
O -3.3078583007 -0.3518099727 0.5480566241
O -1.8441149941 -2.0073969491 0.1397595703
N -1.9672328473 1.5403727742 -0.2372000800
N 3.6044925126 -0.8358440764 -0.6659647320
C 1.1684565146 1.0446332415 -0.4943940738
C 0.1082467096 0.2177955398 0.2395309885
C 2.4785715426 1.1657908669 0.2896724500
C -1.2458520269 0.2676289576 -0.4513144135
C 3.1696429470 -0.1592315605 0.5890169973
C -2.2263428078 -0.8414226742 0.1422529421
H 0.7932826990 2.0569151989 -0.6482792542
H 1.3354698371 0.6191303209 -1.4843783659
H -0.0031461344 0.5661490514 1.2686433794
H 0.3791631733 -0.8378892566 0.2841197320
H 3.1579098277 1.8188328559 -0.2597110183
H 2.2713923792 1.6478155935 1.2450536588
H -1.1432114953 0.0569418065 -1.5170262136
H 2.5004236326 -0.8240708177 1.1341470919
H 4.0493855213 0.0280822082 1.2049984895
H -1.5070190112 2.1488324010 0.4454597884
H -2.1837208522 2.0584218679 -1.0901715209
H 4.2094106392 -0.2068158824 -1.2153183037
H 4.1256865653 -1.6973771969 -0.4514692989
H 2.7834959501 -1.0854874671 -1.2358687369
H -2.8845837684 1.1083956166 0.2016053653
Restarting calculations¶
CENSO keeps track of all performed calculations, if they succeed, fail or are pending. The data is stored in enso.json and enables restarting of CENSO runs. Restarting a calculation is useful if you only considered few conformers in the first run and want to increase the number of investigated conformers (e.g., start from 30 and go to 100 conformers). Or if after a previous calculation of a free ensemble energy, a property, e.g. OR, is to be calculated. This can be done by first calculating the free energy, checking the results and the final ensemble and then restart to calculate the property (OR). Some restart limitations are given though: You can not change anything that concerns the geometry optimization, since all results have to be created with the same method-combination.
When restarting CENSO, files with information of the previous calculation (enso.json, enso_ensemble_partx.xyz, …) are automatically backed up.
Restarting a calculation is performed by calling censo and adjusting the new settings by command line:
# increase the number of considered conformers to 200
$ censo -restart -nc 200 > censo-restart.out &
# or calculate OR after previous free energy calculation
$ censo -restart -OR on > censo-restart-OR.out &
Abbreviations¶
abbreviation |
definition |
|---|---|
SQM |
semiempirical quantum mechanical (method) |
GBSA |
generalized born surface approximation |
DFT |
density functional theory |
DFA |
density functional approximation |
FF |
force field |
CREST |
conformer rotamer ensemble search tool |
CENSO |
command-line energetic sorting |
NMR |
nuclear magnetic resonance |
OR |
optical rotatory dispersion |
GFN |
Geometry Frequency Noncovalent |
GCP |
geometric counterpoise correction |
Introduction to QCxMS¶
Contents
What is QCxMS ?¶
QCxMS is a quantum chemical based program to calculate electron ionization (EI) and collision induced dissociation (CID) mass spectra using Born-Oppenheimer Molecular Dynamics (BO-MD). It is the successor of the QCEIMS program, in which the EI part is exchanged to x to account for the greater general applicibility of the program. However, the program is not available in this form, as it is under review. After publication, the program will be released.
Until then, the QCEIMS version 4.3 is available and free-of-charge at QCEIMS GitHub page
Note
The QCxMS describes the new name for QCEIMS and includes the CID features that are not yet released. However, the EI mode is not influenced hereby. Until publication, QCEIMS version 4.3 the most recent version of the program.
Setting up QCxMS¶
Setup¶
Follow the instructions to use QCxMS without the need of installing or building anything.
Note
The QCxMS describes the new name for QCEIMS and includes the CID features that are not yet released. However, the EI mode is not influenced hereby. Until publication, QCEIMS version 4.3 the most recent version of the program. The setup works the same for both, only the name have to be exchanged.
Untar the zipped archive:
> tar -xvzf QCxMS_5.0.tar.xz
The following files are being extracted:
qceims |
main program (executable) |
pqceims |
script that runs trajectories in parallel locally (executable) |
q-batch |
script that runs trajectories on a cluster with a queueing system (executable) |
getres |
script that gives the status of the parallel QCEIMS production run (executable) |
.mass_raw.agr |
xmgrace template |
.XTBPARAM |
folder involving the xTB-parameterfiles .param_gfn.xtb, .param_gfn2.xtb and .param_ipea.xtb |
EXAMPLE |
folder hosting an example input and coordinate file. |
Place the executables into your
$HOME/bindirectory or path.Place the .XTBPARAM folder and .mass_raw.arg file into your $HOME directory (these files can appear to be hidden).
For easy visualization of the calculated spectra, the Visualization program was developed. It can be found at the PlotMS repository.
Do display the results, we recommend the useage of xmgrace.
Examples for an input file and coordinate file are to be found in the EXAMPLES file.
Quantum Chemistry Codes Required¶
The low cost QC methods GFN1-xTB and GFN2-xTB are implemented in QCxMS. No further rights or installations of third-party software is required and the methods can be called directly by the program. For this reason, using GFN2-xTB is set to run as default.
To run other QC methods, QCxMS needs ORCA or TURBOMOLE to function. If available, place the following QC executables in /usr/local/bin:
MNDO99 |
|
DFTB+ |
place Slater-Koster parameters atom-atom.spl in /usr/local/dftb+ |
ORCA |
All orca utilities must also be in your path. |
TURBOMOLE |
The ridft and rdgrad programs of Turbomole 7.3 are used. |
(xTB) |
Optional. Newer xTB can be called upon if needed. |
Please contact the development teams of these programs directly for executables since we do not have the right to distribute them.
Building the program¶
Note
The QCxMS describes the new name for QCEIMS and includes the CID features that are not yet released. However, the EI mode is not influenced hereby. Until publication, QCEIMS version 4.3 the most recent version of the program. The setup works the same for both, only the name have to be exchanged.
Untar the compressed source archive:
tar -xvzf QCxMS.tar.gz
Enter the newly created folder. All source files can be found in the qcxms folder. To build the program, run the following commands:
cd QCxMS/qcxms/
make
This will build the program and creates the executable in the QCxMS/exe/ folder.
Running QCxMS¶
Contents
The program basically runs in two modes: EI and CID. Both methods require three individual steps to create the final spectrum.
Note
The QCxMS describes the new name for QCEIMS and includes the CID features that are not yet released. However, the EI mode is not influenced hereby. Until publication, QCEIMS version 4.3 the most recent version of the program. For this reason, only the EI part is currently available.
To obtain a QCxMS simulated mass spectrum, please follow this protocol:
Workflow of QCxMS¶
1. Setup¶
Prepare a file with the equilibrium structure of your desired molecule M. For the CID mode, the molecule has to be protonated. This can be done with the protonation tool of CREST (see: CREST command line arguments). Important: The structure file has to be named
coordand should have the TURBOMOLE coord format. In most cases you will have an .xyz file. This file can be easily converted by typingx2t <xyzfile> > coordif you have installed TURBOMOLE. If you do not have TURBOMOLE, you may have to write a script converting .xyz files to TUROBOMOLE coord files. Be advised that the coord file has to be in atomic units.Prepare an input file called qcxms.in. The keywords can be found below and an example is given in in the examples folder. If no such file is prepared, default options are: run GFN1-xTB with 25 × the number of atoms in the molecule trajectories (ntraj).
2. Preparing for Production Runs¶
Run
QCxMSfor the first time. This will generate the first (ground state, GS) trajectory from which information is taken for the production trajectories. Be aware that this already uses the QC method specified. After some steps for equilibration, the files trjM and qceims.gs are generated. It is highly recommended to conduct the initial run with a low-cost method, e.g. GFN1-xTB (default) or OM2-D3.Run
QCxMSfor the second time after the GS run is finished. This genereates the TMPQCEIMS file. If the file qceims.gs exists, this will prepare the specifications for the parallel production run in the TMPQCEIMS folder.
3. Excecuting the Production Runs¶
If you use a computer cluster with a queing system, type
q-batchfor the execution of the batch script. This will initiate the production run with ntraj trajectories. For each trajectory this starts a single core calculation. Reminder: Look into the q-batch script, as it might need to be changed to match for your queing system. If you want to run QCxMS locally, use thepqceimsscript. You might want to leave your work station and even log out in the meantime. In this case, type, where<proc>referres to the number of processors your workstation is allowed to use:
nohup pqceims <proc> &
Optionally, check the status of your QCxMS run by changing to your working directory and typing
getres, which will provide an output of the form:
XXX runs done and written to tmpqceims.res/out
The steps that are conducted in the production runs are displayed in the following figure. For details look into the qceims.out file provided after the calculations are finished. For details on individual runs, look into the TMPQCEIMS/TMP.X folder.
Steps during the production runs in the EI and CID modules. CID module not yet available,¶
Input keywords in qceims.in¶
If no input file is given, default settings are taken. This means an EI calculation is conducted. The general qceims.in input file can be manipulated by providing <parameters> :
<Parameter> |
Specification |
Default |
Alt. settings |
<method> |
Mass Spec. Method |
ei |
cid, dea |
<program> |
QC Program |
xtb |
tmol, orca, mndo, dftb |
<method> |
QC Method |
xtb |
see: Input Details |
<qc settings> |
Basisset and/or Functional |
pbe0 sv(p) |
see: Input Details |
<ip method> |
Ionization Potential Method |
ip-xtb, ip-xtb2 |
ip-tmol, ip-orca, ip-mndo |
ntraj <integer> |
Number of trajectories |
25 × no. of atoms |
<integer> |
tmax <real> |
Maximum MD time |
5 ps |
<integer> |
tinit <real> |
Initial Temperature |
500 K |
<real> |
While xTB is set as default programm and method, it is not required to define it twice.
EI method specific keywords¶
<Parameter> |
Specification |
Default |
Alt. settings |
<mo method> |
Molecular Orbital |
mo-xtb |
mo-orca |
eimp0 <real> |
Electron-beam impact energy |
70 eV |
<real> |
ieeatm <real> |
Impact excess energy (IEE) per atom |
0.6 eV/atom |
<real> |
poisson or gauss (<real> <real>) |
IEE distribution type |
poisson |
<real> |
Note
Poisson/Gauss IEE distribution: Generated from the MO spectrum of the molecule. For low ionization energies and for large molecules, the Poisson distribution may sometimes not converge. Switch to the Gauss distribution by specifying the gauss keyword. Two parameters may be entered, which manipulate the shape of the distribution. Caution! Manipulating the IEE distribution can lead to unphysical spectra with either over- or under-fragmentation of the precursor ion.
CID method specific keywords¶
Note
The QCxMS describes the new name for QCEIMS and includes the CID features that are not yet released. However, the EI mode is not influenced hereby. Until publication, QCEIMS version 4.3 the most recent version of the program. For this reason, this section is not yet available and still undergoes changes.
<Parameter> |
Specification |
Default |
Alt. settings |
<run-type> |
Run-type specifics |
fullauto |
collauto, temprun |
elab <real> |
Collision Energy E(LAB) |
25 eV |
<real> |
eexact |
do not distribute E(coll) |
off |
none |
iatom <string> |
Neutral gas atom |
ar |
he, ne, kr, xe, n2 |
esi or tscale <real> |
E(int) or Temp. scaling |
mol. size (auto) |
<real> |
noesi |
switch off E(int) scaling |
off |
none |
pgas <real> |
gas pressure (Pa) |
0.132 (=1mTorr) |
<real> |
lchamb <real> |
coll. cell length (m) |
0.25 (=25cm) |
<real> |
simmd <integer> |
MD steps for mean-free-path |
10000 (=5ps) |
<integer> |
setcoll <integer> |
number of pgc and fgc |
10 (collauto) |
<integer> |
maxcoll <integer> |
number of pgc, no fgc |
10 (collauto) |
<integer> |
collsec <int> <int> <int> |
number of fragmentations |
0 0 0 |
<integer> |
The run-types can be manipulated by different settings. For Fullauto (general activation mode), lChamb and PGas are important for the number of
precursor-gas collisions (pgc) and fragment-gas collisions (fgc), in the Collauto run-type (forced activation mode), the number of colllisions
can be set to a total number of collisions (pgc + fgc -> setcoll) or only precursor-gas collisions (pgc -> maxcoll).
Misc keywords¶
isotope <atomnumber> <mass_isotope> <atomnumber> <mass_isotope> … |
Switches <atom> <mass> to simulate isotopes. (integer masses) |
iseed <integer> |
Random number seed (Default: 42) |
etemp <real> |
Electronic temperature of convergenc of MD (Default: Auto) |
nfragexit <integer> |
Stop at <integer> simultaneously created fragments (Default: 3) |
ecp / no-ecp |
Use ECPs / Do not use ECPs (ORCA /TMOL only!) |
Input Details¶
QC Programs:¶
Keyword |
Program |
Specifics |
xtb |
xTB 5.8.1 |
built-in GFN1-xTB Hamiltonian |
xtb2 |
xTB 5.8.1 |
built-in GFN2-xTB Hamiltonian |
tmol |
TURBOMOLE |
The ridft and rdgrad programs are called.distribution type |
orca |
ORCA |
large QC program package free for academic use. distribution type |
mndo |
MNDO99 |
semiempirical QC program available from Walter Thiel |
dftb |
DFTB+ |
semiempirical tight-binding QC program free for academic use |
SQM Programs:¶
The GFN1- and GFN2-xTB methods are available without any third-party software. All other semi-empirical quantum mechanical (SQM) methods have to be explicitly called with their corresponding program:
Keyword |
SQM Method |
Program |
Specifics |
xtb |
GFN1-xTB |
QCxMs |
D3-dispersion |
xtb2 |
GFN2-xTB |
QCxMS |
D4-dispersion |
om2 |
OM2-D3 |
MNDO99 |
D3-dispersion |
om3 |
OM3-D3 |
MNDO99 |
D3-dispersion |
am1 |
AM1-D3 |
MOPAC |
D3-dispersion |
pm3 |
PM3-D3 |
MOPAC |
D3-dispersion |
pm6 |
PM6-DH2 |
MOPAC |
D2-dispersion + h-bond |
dftb |
DFTB3-D3 |
DFTB+ |
D3-dispersion |
To decide which method should be used, it is recommended to read the original publication first! For using GFN1-xTB and GFN2-xTB with QCxMS, refer to the publications 4,5.
Note
The usage of AM1 or PM3/PM6 are not recommended, due to their bad performances!
Available Functionals in ORCA/TURBOMOLE:¶
Keyword |
Method |
DFT type |
Availability |
pbe |
PBE-D3BJ |
GGA |
ORCA / TURBOMOLE |
pbe0 |
PBE0-D3BJ |
global hybrid |
ORCA / TURBOMOLE |
pbeh3c |
PBEh3-c |
global hybrid |
ORCA |
revpbe |
REVPBE-D3BJ |
GGA |
ORCA |
blyp |
BLYP-D3BJ |
GGA |
ORCA / TURBOMOLE |
b3lyp |
B3LYP-D3BJ |
global hybrid |
ORCA / TURBOMOLE |
tpss |
TPSS-D3BJ |
meta-GGA |
ORCA / TURBOMOLE |
b97d |
B97-D3BJ |
GGA |
ORCA / TURBOMOLE |
bp86 |
BP86-D3BJ |
GGA |
ORCA / TURBOMOLE |
b3pw91 |
B3PW91-D3BJ |
global hybrid |
ORCA |
m062x |
M062X |
meta-GGA global hybrid |
ORCA / TURBOMOLE |
pw6b95 |
PW6B95-D3BJ |
meta-GGA global hybrid |
ORCA / TURBOMOLE |
Available Basissets in ORCA/TURBOMOLE:¶
Keyword |
Basisset type |
Specification |
Availability |
sv |
double \(\zeta\) |
Split-valence (SV) |
ORCA / TURBOMOLE |
svx |
double \(\zeta\) + pol. |
SV + pol. func. on O,N |
ORCA |
sv(p) |
double \(\zeta\) + pol. |
SV + pol. func. on all except H |
ORCA / TURBOMOLE |
svp |
double \(\zeta\) + pol. |
SV + pol. func. on all |
ORCA / TURBOMOLE |
tzvp |
triple \(\zeta\) + pol. |
TZ + pol. func. on all |
ORCA / TURBOMOLE |
qzvp |
quad. \(\zeta\) + pol. |
QZ + pol. func. on all |
ORCA / TURBOMOLE |
def2-sv(p) |
double \(\zeta\) + pol. |
SV + pol. func. on all except H |
ORCA / TURBOMOLE |
def2-svp |
double \(\zeta\) + pol. |
SV + pol. func. on all |
ORCA / TURBOMOLE |
def2-svpd |
double \(\zeta\) + pol. + diff. |
SV + pol. and diff. func. on all |
TURBOMOLE |
def2-tzvp |
triple \(\zeta\) + pol. |
TZ + pol. func. on all |
ORCA |
def2-tzvpd |
triple \(\zeta\) + pol. + diff. |
TZ + pol. and diff. func. on all |
TURBOMOLE |
def2-qzvp |
quad. \(\zeta\) + pol. |
QZ + pol. func. on all |
ORCA / TURBOMOLE |
ma-def2-svp |
double \(\zeta\) + pol. |
min. aug. SV + pol. func. on all |
ORCA |
ma-def2-tzvp |
triple \(\zeta\) + pol. |
min. aug. TZ + pol. func. on all |
ORCA |
ma-def2-tzvpp |
triple \(\zeta\) + pol. + pol. |
min. aug. TZ + 2x pol. func. on all |
ORCA |
ma-def2-qzvp |
quad. \(\zeta\) + pol. |
min. aug. QZ + pol. func. on all |
ORCA |
Command line Options¶
- -c
check IEE but do nothing (requires ground state trajectory). Writes IEE distribution in file eimp.dat.
- -p
production (fragmentation) mode. Possible in any existing TMPQCEIMS/TMP.XXX directory.
- -eonly
use the requested QC (as specified in qceims.in) and do a single-point energy.
- -e0
same as above, charge = 0
- -e1
same as above, charge = 1
- -qcp <string>
<string> = path to the QC code. /usr/local/bin is default
- -unity
enforces uniform velocity scaling during the vibrational heating phase (in EI mode only)
Visualization¶
Plotting Mass Spectra¶
The PlotMS utility is provided in order to visualize your results. The newest version can be found in the PlotMS repository. The program analyzes the qcxms.res file and combines the results using the ~/.mass_raw.agr template file to create the mass.agr and the results.jdx files.
This may be useful to check for convergence in case you are running more trajectories than actually needed for good statistics. You can plot your spectra as soon as the production run has started.
Change into your working directory and run
plotms. This should generate the mass.agr file.With the mass.agr file, visualize your QCxMS spectrum with:
xmgrace mass.agr
For a comparision of EI spectra, the experimental spectrum can be downloaded from the NIST database if available (JCAMP-DX format). Copy it to the working directory as exp.dat. PlotMS reads the exp.dat and compares your calculated spectrum directly to the experiment (inverted). There is currently no feature to do this for the CID spectrum as well.
Visualization of Trajectories¶
Trajectories are saved in the TMPQCXMS/TMP.XXX directories, where NUM is the first number of the specific
trajectory track to be visualized. There are two programs that can easily display the trajectories, which
are saved in the trj.NUM.xxx files. One is (g)molden, the other is VMD. Obtaining a video (.avi) of a
given trajectory is possibly most easily done by loading the trajectory of choice into VMD (file type .xyz).
The msmovie and movie.tcl scripts for VMD generate a visualization using the dynamic bonds graphical representations
setting. This allows for movie generation employing the VMD movie maker plug-in. Simply type msmovie X Y in the
working directory to load the trajectory TMPQCEIMS/TMP.X/trj.X.Y. For instance, msmovie 1 1 loads the first
trajectory of the first folder.
Some adjustments according to personal preferences for movie-making may have to be made in these scripts.
Quickstart¶
The default settings of QCxMS provide a good starting point for the calculations. However, if more control for Running QCxMS is needed, example input files for each run type can be found below.
EI - positive Ion Electron Ionization¶
ei
xtb
ntraj xxx
tmax xxx
DEA - negative Ion Electron Ionization¶
dea
scan 1
upper 15
lower 0
<functional>
<basis>
Instead of the IEE distribution, the excess energy is scanned by switching on the scan keyword, with upper/lower bounds in eV. The negative ion mode is enabled with the the xtb method or the orca program for DFT methods. The ma-def2-SVP/ma-def2-TZVP basis sets are recommended for anion calculations. The xtb negative ion simulations are not recommended for production level for accuracy reasons.
CID - positive Ion Collision Induced Dissociation¶
Note
The QCxMS describes the new name for QCEIMS and includes the CID features that are not yet released. However, the EI mode is not influenced hereby. Until publication, QCEIMS version 4.3 the most recent version of the program. For this reason, this section is not available yet.
cid
xtb2
eimpact 60
lchamb 0.25
fullauto
The run-type must explicitly be defined so the program knows how to handle the number of collisions.
News¶
% will be replaced by ablog
Versions and Changelog¶
Note
Release candidates and beta versions are not listed here.
- Version 6.2
Bugfix: Fukui index calculation
Bugfix: wrong forces in FIRE optimizer
Bugfix: $cube instructions were not read
Bugfix: Input error for
$gbsadata groupGFN0-xTB Hamiltonian consistent with ChemRxiv preprint
periodic boundary conditions for GFN0-xTB
preliminary implicit solvation model GBSA for GFN0-xTB
- Version 6.1.4
Bugfix: parallisation error in GBSA
- Version 6.1.3
added FIRE and L-ANCopt as optimization engines
Bugfix: FOD calculation was using wrong density
- Version 6.1.2
Bugfix: wrong convergence threshold for RF solver
- Version 6.1.1
Bugfix: wrong constraining energy in
xtbscan.logBugfix: symmetry finder was inactive
- Version 6.1
removed
isotopeinputTurbomole
basisandmosprintoutORCA GBW file printout
metadynamics runtyp added
GFN0-xTB implemented
completely tunable model Hessian for optimizer
separated fixing and constraining
elementwise fixing and constraining
new geometry summary printout for optimizations
better printout for optimizer (RMSD, energy gain)
profiling printout for SCC and optimizer
adjustable SASA grid for GBSA
case insensitive solvent strings for GBSA
Bugfix: mode following printout crashes for large systems (>100 atoms)
- Version 6.0.2
Bugfix: timings wrapped around
- Version 6.0.1
additional GFN2-xTB GBSA parameteres added
Bugfix:
molden.inputcould not be disabledBugfix: deallocation error in mode following
- Version 6.0
GFN2-xTB GBSA parameteres added
internal parameter files
detailed input
XTBPATHvariableparallel Hessian with GBSA
logfermi wallpotential added
sdf input files supported
automatic Fukui indices and electrophilicity index
License¶
This work is licensed under the Creative Commons Attribution-ShareAlike 4.0 International (CC BY-SA 4.0). To view a copy of this license, visit creative commons or send a letter to Creative Commons, PO Box 1866, Mountain View, CA 94042, USA.
Need Help¶
If you’re heading trouble please contact xtb@thch.uni-bonn.de