CREST(1)

📦 version 2.12, in fedora 43, fedora 44

✨ CREST ✨ (1)

okay bestie, sit down, hydrate, because this is the manual page for crest 💖 it's the Conformer-Rotamer Ensemble Sampling Tool, and it runs on the GFN methods. yes it's a lot of options. no you're not going to read them all in one sitting. we're getting through it together tho 🫶

🌸 NAME 🌸

crest — the Conformer-Rotamer Ensemble Sampling Tool, built on top of the GFN methods. that's it, that's the name, she's iconic 💅

🦋 SYNOPSIS 🦋

crest [INPUT] [OPTION]...

💜 DESCRIPTION 💜

so like, crest is the Conformer-Rotamer Ensemble Sampling Tool based on the GFN methods. that's the whole vibe.

it uses the xTB program, and it's compatible with xTB version 6.4.0. no cap.

if you use this code in your work, you gotta cite it, periodt:

P. Pracht, F. Bohle, S. Grimme, PCCP, 2020, 22, 7169-7192.

and  S. Grimme, JCTC, 2019, 15, 2847-2862.

with help from:
F.Bohle, S.Ehlert, S.Grimme, P.Pracht

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. 💀 yes that's the real legal vibe, we keep it, it matters.

🎀 OPTIONS 🎀

the FIRST argument CAN be a coordinate file in the TM format (coord, Bohr) or in the Xmol format (*.xyz, Ang.). and if there's no such file sitting there as the first argument? crest will just go looking for a file called coord in the TM format on its own. she's proactive like that ✨

🧚 General and technical options

  • -v1 — use the MF-MD-GC workflow. (OUTDATED 🫠)
  • -v2 — use the MTD-GC workflow. (OUTDATED 🫠)
  • -v3 (or -v2i) — use the iMTD-GC workflow. [default] 👑
  • -v4 — use the iMTD-sMTD workflow.
  • -entropy — same workflow as -v4, but specialized for calculating conformational entropy. 🌈
  • -xnam bin — specify the name of the xtb(1) binary that should be used.
  • -niceprint — progress bar printout for optimizations. cute and useful 💖
  • -dry — perform a "dry run". it only prints the settings that would be applied with the CMD input and stops the run before any calculations happen. window shopping, essentially 🛍️
  • -T int — set total number of CPUs (threads) to be used. parallel settings are then determined automatically for each step. if it's not set by -T, this number is read from the OMP_NUM_THREADS global variable.

🔥 Calculation options

  • -g string — use GBSA implicit solvent for solvent string.
  • -alpb string — use ALPB implicit solvent for solvent string.
  • -chrg int — set the molecules' charge.
  • -uhf int — set int=N alpha - N beta electrons
  • -nozs — do not perform z-mat sorting. [default]
  • -opt lev — set optimization level for ALL GFN-xTB optimizations. [default: vtight]
    • lev = vloose, loose, normal, tight, vtight
  • -gfn1 — use GFN1-xTB.
  • -gfn2 — use GFN2-xTB. [default]
  • -gff, -gfnff — use GFN-FF (requires xtb(1) 6.3 or newer). (for GFN-FF searches, bond constraints are applied automatically.)
  • -gfn2//gfnff — GFN2-xTB//GFN-FF composite mode. 🧬

💫 Adding additional constraints to the calculations:

the user is able to include additional constraints to ALL xtb(1) calculations that are conducted by CREST.

  • -cinp file — read in a file containing the constraints. constraints have to be in the same format as in xtb(1). (this was done previously via the .constrains file.)
  • -cbonds — define automatic bond constraints (set up from topology).
  • -nocbonds — turn off -cbonds. (for GFN-FF, mainly. see above.)
  • -fc float — define force constant for defined constraints (-cbonds).

🌈 Options for ensemble comparisons

  • -cregen file — use ONLY the CREGEN subroutine to sort a given ensemble file.
  • -ewin real — set energy window in kcal/mol. [default: 6.0 kcal/mol]
  • -rthr real — set RMSD threshold in Ang. [default: 0.125 Ang]
  • -ethr real — set E threshold in kcal/mol. [default: 0.05 kcal/mol]
  • -bthr real — set Rot. const. threshold. [default: 0.01 (= 1%)]
  • -pthr real — Boltzmann population threshold. [default: 0.05 (= 5%)]
  • -temp real — set temperature in CREGEN. [default: 298.15 K]
  • -prsc — create a scoord.* file for each conformer.
  • -nowr — don't write new ensemble files.
  • -eqv, -nmr, -entropy — compare nuclear equivalences (requires rotamers).
  • -cluster int — PCA and k-Means clustering of sorted ensemble. works as an extenstion to the CREGEN sorting. int is the number of clusters to be formed.
  • -notopo — turn off any topology checks in CREGEN.

🦋 Options for the iMTD-GC workflows

  • -cross — do the GC part. [default]
  • -nocross — don't do the GC part.
  • -shake int — set SHAKE mode for MD. (0=off, 1=H-only, 2=all bonds) [default: 2]
  • -tstep int — set MD time step in fs. [default: 5 fs]
  • -mdlen/-len real — set MD length (all MTDs) in ps. also possible are multiplicative factors for the default MD length with xreal.
  • -mddump int — xyz dumpstep to Trajectory in fs. [default: 100 fs]
  • -vbdump real — set Vbias dump frequency in ps. [default: 1.0 ps]
  • -tnmd real — set temperature for additional normal MDs. [default: 400 K]
  • -norotmd — don't do the regular MDs after the second multilevel optimization step.
  • -quick — perform a search with reduced settings for a crude ensemble.
  • -squick — perform a even further reduced search.
  • -mquick — perform a search with maximum reduced settings. (do not reduce the settings more than that.) 🫣
  • -origin — track the step of generation for each conformer/rotamer. [default]
  • -keepdir — keep sub-directories of the conformer generation step.
  • -nci — generate an ellipsoide potential around the input structure and add it to the MTD simulation. this can be used to find aggregates of NCI complexes.
  • -wscal real — scale the ellipsoide potential axes by factor real.

🌡️ Thermostatistical options (used in entropy mode)

  • -trange lower upper step — entropies are calculated for different temperatures. these are calculated in a temperature range from lower to upper with step in between. [default: 280K-380K in 10K steps]
  • -fscal float — frequency scaling factor. [default: 1.0]
  • -sthr float — vibrational/rotational entropy interpolation threshold (tau). [default: 25.0 cm^-1]
  • -ithr float — imaginary mode inversion cutoff. [default: -50.0 cm^-1]
  • -ptot float — sum of population for structures considered in msRRHO average. [default: 0.9 (= 90%)]

🛠️ Other tools for standalone use

  • -zsort — use only the zsort subroutine to sort the z-matrix of the input coordinate file.
  • -mdopt file — optimize along trajectory or ensemble file in the XYZ format. each point on the file is optimized.
  • -screen file — optimize along ensemble file in the XYZ format. a multilevel optimization is performed with continiously increasing thresholds. after each step the ensemble file is sorted.
  • -protonate — find a molecule's protomes by using a LMO pi- or LP-center approach.
  • -deprotonate — find a molecule's deprotomers.
  • -tautomerize — combine the protonation and deprotonation to find prototropic tautomers.
    • -trev — do first the deprotonation and then the protonation in the -tautomerize mode, i.e., reverse of the default procedure.
    • -iter int — set number of protonation/deprotonation cycles in the tautomerization script. [default: 2]
  • -compare f1 f2 — compare two ensembles f1 and f2. both ensembles must have the same order of atoms of the molecule and should contain rotamers.
    • -maxcomp int — select the lowest int conformers out of each ensemble to be compared with -compare. [default: 10]
  • -testtopo file — analyze some stuctural info (topology) for a given file.
  • -constrain atoms — write example file .xcontrol.sample for constraints in crest. (see -cinp option above.)
  • -thermo file — calculate thermo data for given structure. also requires vibrational frequencies in the TM format, saved as file called vibspectrum.
  • -rmsd, -rmsdheavy file1 file2 — calculate RMSD or heavy atom RMSD between two structures. input coords are automatically transformed to Angstroem.
  • -splitfile file [from] [to] — split an ensemble from file into seperate directories for each structure. from and to can be used to select specific structures from the file. the new directories are collected in the SPLIT directory.

📝 NOTES 📝

want the literature references? just hit --cite. easy 💅

👑 AUTHORS 👑

  • P.Pracht
  • S.Grimme

Universitaet Bonn, MCTC 🌸

and that's the whole page, bestie 🫶 this one's Crest 2.11.0, dated 2025-07-23, and yes, it's a CREST(1) manual page, so go forth and sample those conformers. slay 💖✨

📦 where this page comes from