QCG Keywords
This page contains the documentation of available keywords for QCG. Required arguments will be marked with < >, optional arguments are marked by brackets [ ].
Table of contents
The QCG extension of CREST can be invoked via the command line. To activate QCG, use a command similar to
crest <SOLUTE> -qcg <SOLVENT> [OPTIONS]
Two files containing <SOLUTE> and <SOLVENT> coordinates have to be provided that can be in any format supported by CREST. The general and technical command line options of CREST also apply for the QCG runtype (see Keyword Documentation). Take care to always set the number of cores with --T <INT>. The [OPTIONS] that can be used in conjunction with -qcg are documented below.
QCG Runtypes
| Runtype | Command | Description |
|---|---|---|
| Grow algorithm | --grow | The [default] runtype of QCG. The grow algorithm is employed without ensemble generation. See here. |
| Ensemble algorithm | --ensemble | The grow algorithm is employed with ensemble generation. See here. |
| Solvation Free Energy | --gsolv | Generates ensembles to compute the solvation free energy. See here. |
Grow Algorithm Options
Important: Without setting a number of solvents that should be added, QCG will add solvent molecules until the interaction energy converges. As this is often difficult, it might occur that the program will not stop adding solvents. It is highly recommended to always define a number of solvent molecules that should be added with
--nsolv <INT>.| Command | Description |
|---|---|
--nsolv <INT> | Number of solvents that should be added. |
--nopreopt | Does not perform a GFN2-xTB preoptimization of the input structures. |
--keepdir | Saves the temporary directories of QCG calculations. |
--gfn1, --gfn2, --gfnff | Use GFN1-xTB, GFN2-xTB [default], or GFN-FF for geometry optimization during the QCG Grow algorithm. |
--samerand | Use the same random number for the xTB-IFF runs. |
--chrg <INT> | Set the charge for the solute and creates .CHRG file. |
--uhf <INT> | Set the number of unpaired electrons for the solute and creates .UHF file. |
--wscal <REAL> | Set the scaling factor for the outer wall potential. The default is 1.0 except for water. |
--fixsolute | Fix the solute during the grow process (automatically done for water as solvent). |
--nofix | No fixing of the solute during the grow process (fixing is only applied for water as solvent file). |
--xtbiff | Use the old xtbiff binary for docking instead of the recommended aISS algorithm available with xtb. The xtbiff can be obtained at the xtbiff GitHub repository . |
--normdock | Use the docking algorithm during the grow algorithm with normal settings (per default, reduced settings are applied for a faster search). This is only possible in combination with the aISS algorithm. |
--directed <FILE> | Employ the directed docking feature of the aISS algorithm implemented in xtb to solvate specific atoms of the solute. For details about the format of <FILE> see here. |
Ensemble Algorithm Options
| Command | Description |
|---|---|
--qcgmtd | Perform an ensemble generation with the NCI-MTD runtype with parameters adjusted for solutions. [default] |
--ncimtd | Perform an ensemble generation with the NCI-MTD runtype. |
--mtd | Perform an ensemble generation with a single MTD simulation. |
--md | Perform an ensemble generation with a single MD simulation. |
--enslvl gfn1, --enslvl gfn2, --enslvl gfnff | Use GFN1-xTB, GFN2-xTB [default], or GFN-FF for MD or MTD simulation and geometry optimizations during the ensemble generation. For the NCI-MTD runtype GFN-FF is the [default]. |
--len <REAL>, --mdlen <REAL>, --mdtime <REAL> | Set the MD or MTD length in ps. |
--mddump <INT> | Set the dumping frequency of the MTD simulations. |
--tstep <INT> | Set the MD or MTD time step in fs. |
--vbdump <INT> | Set the dumping interval (in ps) for which a new reference structure is taken for the bias potential. |
--norotmd | Turn off the additional MDs on the lowest conformers after the MTD simulations in the NCI-MTD runtype. |
--tnmd <REAL> | Set the temperature for the additional MDs in the NCI-MTD runtype. |
--mreset <INT> | Set maximum number of MTD restarts of the NCI-MTD run-type |
---fin_opt_gfn2 | Perform final GFN2-xTB optimization after grow step and evaluate ensemble after ensemble step with GFN2-xTB. Only applicable if GFN2-xTB is not used for grow and ensemble step. |
Solvation Free Energy Options
| Command | Description |
|---|---|
--nocff | Generate the reference ensemble with the same method the solute–solvent ensemble was generated instead of the CFF algorithm |
--esolv | Compute only the pure solvation energy without frequency calculations. |
--nclus [INT] | Set the number of solute–solvent clusters to take further into account. The highest populated clusters are considered. If [INT] is not set, a number is determined according to the population distribution (max. 10). |
--freqlvl gfn1, --freqlvl gfn2, --freqlvl gfnff | Use GFN1-xTB, GFN2-xTB, or GFN-FF [default] for frequency in QCG solvation free energy calculations. |
--freqscal <REAL> | Only for printout: Set a scaling factor for the translational and rotational entropy. [default] is <REAL>=0.75. |