# Basic Usage¶

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 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 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 Iterative version of the MTD-GC workflow, which is the default runtype of CREST.
CREGEN ensemble sorting tool
flag: -cregen  Tool to sort a given ensemble  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 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  Optimize each point on a given trajectory or ensemble file  with GFNn–xTB.
SCREEN ensemble screening tool
flag: -screen  Optimize each point on a given trajectory or ensemble file  with GFNn–xTB in a multilevel approach and sort the resulting ensemble (CREGEN).
Other structure screening modes
flag: -protonate 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. -deprotonate A tool to find deprotomers of the input structure. Each H atom is removed and the resulting structures are optimized and sorted. -tautomerize 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.