Basic Usage ¶

Contents

Basic Usage
- Runtypes
- Options

CREST is usually invoked via commandline, and requires only a coordinate input file. The program supports the TURBOMOLE coordinates (coord, Bohr) and Xmol (*.xyz, Angstroem) format 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. The different [OPTIONS] are listed below and refer to Version 2.7 of the CREST code.

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

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

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`.

CREGEN ensemble sorting tool

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.

ZSORT z-matrix sorting tool

flag:	`-zsort`
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:	`-mdopt <FILE>`
description:	Optimize each point on a given trajectory or ensemble file `<FILE>` with GFNn–xTB.

SCREEN ensemble screening tool

flag:	`-screen <FILE>`
description:	Optimize each point on a given trajectory or ensemble file `<FILE>` with GFNn–xTB in a multilevel approach and sort the resulting ensemble (CREGEN).

Other structure screening modes

flag:	`-protonate`
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.
flag:	`-deprotonate`
description:	A tool to find deprotomers of the input structure. Each H atom is removed and the resulting structures are optimized and sorted.
flag:	`-tautomerize`
description:	A tool that combines the `-protonate` and `-deprotonate` options to find (prototropic) tautomers of the input structure.

Options ¶

General Options ¶

-h, -help

Show help page

-chrg INT: Specify molecular charge as INT, overrides .CHRG file
-uhf INT: Specify \(N_{\alpha}-N_{\beta}\) as INT, overrides .UHF file

`-gfn0`	Use GFN0-xTB
`-gfn1`	Use GFN1-xTB

-gfn2 [DEFAULT]: Use GFN2-xTB, which is the default.

-gff

Use GFN-FF (only xtb 6.3 and newer)

-g, -gbsa SOLVENT: 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.
-opt LEVEL: Set the optimization accuracy for final GFNn–xTB optimizations. See Geometry Optimization for valid LEVEL arguments. The [DEFAULT] is vtight.
-zs [DEFAULT]: Perform z-matrix sorting (i.e. ZSORT) for the input coordinate file.

-nozs

Do not perform z-matrix sorting of the input file.

-ewin REAL: 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).
-xnam BIN: Specify the name (and path) of the xtb binary that sould be used as BIN. The [DEFAULT] is xtb.

`-prsc`	Create a scoord.`*` file for each conformer in the `TURBOMOLE` format.
`-niceprint`	In-line progress bar printout for optimizations.

-scratch <DIR>: Performs the entire calculation in the specified <DIR>. If <DIR> is not existing it will be created.

`-T INT`	Specify the number of CPU threads INT that shall be used. `CREST` automatically adjusts the number of processes according to this variable in each step, in order to achieve optimal parallelization of the calculations.
`-dry`	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.

Options for MF-MD-GC ¶

Warning

The MF-MD-GC workflow is outdated

`-nomf`	Skip modefollowing
`-nomd`	Skip MD part
`-nocross`	Skip genetic crossing part.
`-loose`	Decrease used number of selected modes
`-vloose`	Decrease used number of selected modes a lot
`-tight`	Increase used number of selected modes

-mdlen, -len REAL: Set length of the molecular dynamics simulation to REAL ps. The [DEFAULT] is 40 ps.
-shake INT: Set SHAKE mode for MD. INT can be 0(= off), 1(= H-only), 2(= all bonds) The [DEFAULT] is 2.

-quick

Conduct only one MF/MD (no GC) run to obtain a crude conformer ensemble.

Options for iMTD-GC ¶

-cross [DEFAULT]: Do the genetic structure crossing (GC) part.

-nocross

Don´t do the GC part.

-mrest INT: Maximum number of MTD restarts in iMTD-GC algorithm. The [DEFAULT] is 5 cycles.
-shake INT: Set SHAKE mode for MD. INT can be 0(= off), 1(= H-only), 2(= all bonds) The [DEFAULT] is 2.
-tstep INT: Set MD time step to INT fs. The [DEFAULT] is 5 fs.
-mdlen, -len REAL: Set length of the meta-dynamics simulations (MTD) to REAL ps. The [DEFAULT] is depending on the size and flexibility of the system.
-mddump INT: Set dumpstep in which coordinates are written to the trajectory file to INT fs. The [DEFAULT] is 100 fs.
-vbdump REAL: Set dump frequency in which a new reference structure is taken for \(V_{bias}\) to REAL ps. The [DEFAULT] is 1.0 ps.
-tnmd REAL: Set temperature for the additional normal MDs on the lowest conformers after the MTD step. The [DEFAULT] is 400 K.

`-norotmd`	Don´t do the additional MDs on the lowest conformers after the MTD step.
`-quick`	Perform a search with reduced settings for a crude conformer ensemble.
`-squick, -superquick`
	Perform an even more crude conformational search than with `-quick`.
`-mquick`	Perform an even more crude conformational search than with `-quick` or `-squick`.

-origin [DEFAULT]: Track the step of generation for each conformer/rotamer.

`-keepdir`	Keep sub-directories of the conformer production run.
`-nci`	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.

-wscal REAL: Scale the ellipsoide potential axes in the NCI mode by factor REAL.

Options for CREGEN ¶

Note

The CREGEN routine is also used to sort in between the steps of the conformational searches. Therefore the following options also affect the performance of the two conformer algorithms.

-rthr REAL: Set RMSD threshold in Ångström. The [DEFAULT] is 0.125 Å.
-ethr REAL: Set energy threshold between conformer pairs in kcal/mol. The [DEFAULT] is 0.10 kcal/mol.
-bthr REAL: Set Rotational constant threshold to REAL. The [DEFAULT] is 0.02.
-athr REAL: Similarity threshold to determine internal rotation equal atoms for NMR. The [DEFAULT] is 0.04.
-pthr REAL: Boltzmann population threshold. The [DEFAULT] is 0.05 (= 5%).
-temp REAL: Set temperature for the calculation of Boltzmann weights. The [DEFAULT] is 298.15 K.

`-nmr, -eqv`	Activate determination and printout of NMR-equivalencies. Writes the files `anmr_rotamer` and `anmr_nucinfo`, which are required by the `ENSO` python script.
`-esort`	Sort only based on energy (i.e., no RMSD and rotational constant comparison)
`-nowr`	Don´t write new ensemble files (crest_rotamers_`*`.xyz, crest_conformers.xyz)
`-rot`	Use only rotational constant for checks (and no RMSD)
`-subrmsd`	Compare only those parts of the structure that were also included in the metadynamics bias potential. Can be important for constrained conformational searches.

Options for other modes ¶

-compare <FILE1> <FILE2>: Compare two ensembles <FILE1> and <FILE2>. Both ensembles must have the same order of atoms of the molecule and should contain rotamers.
-maxcomp INT: Selcect the lowest INT conformers out of each ensemble to be compared with -compare. The [DEFAULT] is the 10 lowest conformers.
-iter INT: Number of Protonation/Deprotonation Iterations for -tautomerize mode. The [DEFAULT] is 2 iterations.
-swel STR: Change H\(^+\) in the protonation tool to some other ion specified by STR. STR has to contain the element symbol AND charge, e.g. Na+

-trev

For the tautomerization mode rverse the order of protonation/deprotonation steps. I.e., first deprotonate the molecule and then protonate it again

Options for the PROPERTY mode ¶

Note

The PROPERTY mode automatically performs additional calculations on the final conformer ensemble after the iMTD-GC (or a given input ensemble, see flag -forall)

-prop STR: This initializes the usage of the “property” mode. STR defines what shall be done with the ensemble. Valid options for STR are currently (case sensitive!):

hess - performs a hessian calculation for all conformers and re-weights the ensemble on free energies

reopt - reoptimization of the ensemble with vtight thresholds (usefull for “quick” runs)

autoIR - calculate vib. modes for all conformers and average them (weighted by Boltzmann populations) in a single “crest.vibspectum” file.

-forall <FILE>: 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.

`--constrain <atom list>`
	Set up an example file in which the atoms in <atom list> shall be constrained. The file will be called `.xcontrol.sample`. No calculations will be performed and the run is aborted after this sample is wirtten.