CREST command line arguments¶
Contents
CREST
is usually invoked via command line, and requires only a coordinate input file.
The program supports the TURBOMOLE
coordinates (coord, Bohr), Xmol (*.xyz, Ångström)
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 technical options¶
Flag |
Description |
---|---|
|
Print an overview of most available options (i.e., this site) |
|
Print only the program header and disclaimer. |
|
Print the most relevant citations. |
|
Specify the name (and path) of the |
|
In-line progress bar printout for optimizations. |
|
Performs the entire calculation in the specified |
|
Specify the number of CPU threads |
|
Perform 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 available 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-matrix sorting function (ZSORT).
The different runtypes are:
Algorithm |
Flag |
Description |
---|---|---|
MF-MD-GC algorithm (outdated) |
|
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MTD-GC algorithm (outdated) |
|
Second generation of the GFNn-xTB driven conformational search algorithm, consisting out of a meta-dynamics approach and genetic structure crossing. |
iMTD-GC algorithm |
|
Iterative version of the MTD-GC workflow, which is the default runtype of |
iMTD-sMTD algorithm |
|
Iterative workflow, making use of static metadynmics simulations. |
Conformational entropy algorithm |
|
Specialized version of the iMTD-sMTD workflow, specialized in the calculation of conformational entropy. |
Ensemble sorting¶
CREGEN ensemble sorting tool for standalone use
Flag |
Description |
---|---|
|
Tool to sort a given ensemble |
|
Set the energy threshold to REAL kcal/mol. This affects several runtypes and the |
|
Create a scoord.`*` file for each conformer in the |
|
Set RMSD threshold in Ångström. The |
|
Set energy threshold between conformer pairs in kcal/mol. The |
|
Set lower bound for the rotational constant threshold to REAL. The |
|
Boltzmann population threshold. The |
|
Activate determination and printout of NMR-equivalencies. Writes the files |
|
Similarity threshold to determine internal rotation of equal atoms for NMR. The |
|
Set temperature for the calculation of Boltzmann weights. The |
|
Sort only based on energy (i.e., no RMSD and rotational constant comparison) |
|
Don’t write new ensemble files (crest_rotamers_`*`.xyz, crest_conformers.xyz) |
|
Compare only those parts of the structure that were also included in the metadynamics bias potential. Can be important for constrained conformational searches. |
|
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 |
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 |
Description |
---|---|
|
Use GFN1-xTB |
|
Use GFN2-xTB |
|
Use GFN-FF (recommended for faster sampling) |
|
Use GFN2-xTB//GFN-FF composite method |
Charge and multiplicity
Flag |
Description |
---|---|
|
Specify molecular charge as INT, overrides |
|
Specify \(N_{\alpha}-N_{\beta}\) as INT, overrides |
Implicit solvation
Flag |
Description |
---|---|
|
Generalized born (GB) model with solvent accessible surface (SASA) model, for available SOLVENT options see Implicit Solvation. The solvent input is not case-sensitive. |
|
New ALPB implicit solvation model, for available SOLVENT options see Implicit Solvation. The solvent input is not case-sensitive. |
Geometry optimization thresholds
Flag |
Description |
---|---|
|
Set the optimization accuracy for final GFNn–xTB optimizations. See Geometry Optimization for valid LEVEL arguments. The |
Options for conformational search algorithms¶
Z-matrix sorting (see also --zsort
above)
Flag |
Description |
---|---|
|
Perform z-matrix sorting (i.e. ZSORT) for the input coordinate file. |
|
|
Genetic Z-matrix crossing
Flag |
Description |
---|---|
|
|
|
Skip Z-matrix structure crossing. |
Additional MD sampling after MTD
Flag |
Description |
---|---|
|
Turn off the additional MDs on the lowest conformers after the MTD step. |
|
Set temperature for the additional normal MDs on the lowest conformers after the MTD step. The |
Adjusting iterative behavior of iMTD-GC
Flag |
Description |
---|---|
|
Maximum number of MTD restarts in iMTD-GC algorithm. The |
Special settings for the iMTD-GC workflow
Flag |
Description |
---|---|
|
Turn a small enhancement routine on/off to rotate OH groups after MTD. The |
|
Maximum number of new structures by the above mentioned enhancement routine. The |
|
Perform a search with reduced settings for a crude conformer ensemble. |
|
Perform an even more crude conformational search than with |
|
Perform an even more crude conformational search than with |
|
Track the step of generation for each conformer/rotamer. |
|
Specialized NCI mode that can be used to find aggregates of NCI complexes. The option generates an ellipsoid 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. |
|
Scale the ellipsoid potential axes in the |
Technical iMTD-GC settings
Flag |
Description |
---|---|
|
Keep sub-directories of the conformer production run. |
Property mode appendix
Flag |
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. |
|
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. |
Valid options for STR are currently (case sensitive!):
Option |
Description |
---|---|
|
performs a hessian calculation for all conformers and re-weights the ensemble on free energies |
|
reoptimization of the ensemble with vtight thresholds (useful for “quick” runs) |
|
calculate vib. modes for all conformers and average them (weighted by Boltzmann populations) in a single “crest.vibspectrum” file. |
Note
The different quick, NCI and property settings are incompatible with --entropy
!
Entropy mode settings
Flag |
Description |
---|---|
|
Specify the ensemble growth threshold (% new conformers) for |
|
Specify the entropy growth threshold (% growth entropy) for |
|
Entropies from the |
|
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%). |
|
Scale frequencies read for \(\overline{S}_{msRRHO}\) by a given factor. Also works together with the |
|
Specify the rotor cutoff for the ro/vib entropy interpolation (\(\tau\)). Also works together with the |
|
Sum of population for structures considered in msRRHO average. The |
Other tools¶
ZSORT z-matrix sorting tool
Flag |
Description |
---|---|
|
The atom order of the given input file is sorted in order to yield a more consistent z-matrix, i.e., atoms are grouped together according to the molecular structure (e.g. methyl groups). |
MDOPT parallel ensemble optimization
Flag |
Description |
---|---|
|
Optimize each point on a given trajectory or ensemble file |
SCREEN ensemble screening tool
Flag |
Description |
---|---|
|
Optimize each point on a given trajectory or ensemble file |
Automated protonation site screening
Flag |
Description |
---|---|
|
A tool that can be used to find protonation sites, i.e., the protomers of the input structure. In the approach first localized molecular orbitals (LMOs) are calculated and LP- and π-centers are identified. Then, a proton is added to each of these centers and the resulting structures are optimized and sorted. |
Modifier |
Description |
---|---|
|
Change H\(^+\) in the protonation tool to some other ion specified by STR. STR has to contain the element symbol AND charge, e.g. |
Automated deprotonation site screening
Flag |
Description |
---|---|
|
A tool to find deprotomers of the input structure. Each H atom is removed and the resulting structures are optimized and sorted. |
Automated tautomerization screening
Flag |
Description |
---|---|
|
A tool that combines the |
Modifier |
Description |
---|---|
|
Reverse order of operation for tautomerization mode, i.e., first deprotonate and then protonate. |
|
Number of Protonation/Deprotonation Iterations for |
Ensemble comparison
Flag |
Description |
---|---|
|
Compare two ensembles <FILE1> and <FILE2>. Both ensembles must have the same order of atoms of the molecule and should contain rotamers (e.g. |
Modifier |
Description |
---|---|
|
Select the lowest INT conformers out of each ensemble to be compared with |
Rovibrational entropy average
Flag |
Description |
---|---|
|
Calculate the \(\overline{S}_{msRRHO}\) term for a specified ensemble. The |
Modifier |
Description |
---|---|
|
Write files with free energy Boltzmann populations for each |
RMSD comparison
Flag |
Description |
---|---|
|
Calculate the RMSD or heavy atom RMSD between two given structures. Input format of the two structures can be any of the formats that can be read by CREST, output will always be the RMSD in Ångström. |
Topology check
Flag |
Description |
---|---|
|
Calculate the topology (neighbour lists) for a given input structure and print to info to screen. |
Thermostatistical calculations from frequencies
Flag |
Description |
---|---|
|
Calculate thermo data for given structure. Also requires vibrational frequencies in the Turbomole format, saved as file called |
Modifier |
Description |
---|---|
|
Splitting an Ensemble into separate files
Flag |
Description |
---|---|
|
Split an ensemble from |