1CREST(1)                         User Commands                        CREST(1)
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NAME

6       crest - Conformer-Rotamer Ensemble Sampling Tool based on the GFN
7       methods
8

SYNOPSIS

10       crest [INPUT] [OPTION]...
11

DESCRIPTION

13       Conformer-Rotamer Ensemble Sampling Tool based on the GFN methods.
14
15       Using the xTB program. Compatible with xTB version 6.4.0.
16
17       Cite work conducted with this code as
18
19            P. Pracht, F. Bohle, S. Grimme, PCCP, 2020, 22, 7169-7192.
20
21            and  S. Grimme, JCTC, 2019, 15, 2847-2862.
22
23            with help from:
24            F.Bohle, S.Ehlert, S.Grimme, P.Pracht
25
26       This program is distributed in the hope that it will be useful, but
27       WITHOUT ANY WARRANTY; without even the implied warranty of
28       MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
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OPTIONS

31       The FIRST argument CAN be a coordinate file in the TM (coord, Bohr) or
32       Xmol (*.xyz, Ang.) format. If no such file is present as the first
33       argument crest will automatically search for a file called “coord” in
34       the TM format.
35
36   General and technical options
37       -v1
38           Use the MF-MD-GC workflow. (OUTDATED)
39
40       -v2
41           Use the MTD-GC workflow. (OUTDATED)
42
43       -v3 (or -v2i)
44           Use the iMTD-GC workflow. [default]
45
46       -v4
47           Use the iMTD-sMTD workflow.
48
49       -entropy
50           The same workflow as with “-v4”, specialized for the calculation of
51           conformational entropy.
52
53       -xnam bin
54           Specify name of the xtb(1) binary that should be used.
55
56       -niceprint
57           Progress bar printout for optimizations.
58
59       -dry
60           Perform a “dry run”. Only prints the settings that would be applied
61           with the CMD input and stops the run before any calculations
62
63       -T int
64           Set total number of CPUs (threads) to be used. Parallel settings
65           are then determined automatically for each step. If not set by
66-T”, this number is read from the OMP_NUM_THREADS global variable.
67
68   Calculation options
69       -g string
70           Use GBSA implicit solvent for solvent string.
71
72       -alpb string
73           Use ALPB implicit solvent for solvent string.
74
75       -chrg int
76           Set the molecules’ charge.
77
78       -uhf int
79           Set int=N alpha - N beta electrons
80
81       -nozs
82           Do not perform z-mat sorting. [default]
83
84       -opt lev
85           Set optimization level for ALL GFN-xTB optimizations. [default:
86           vtight]
87
88lev = vloose, loose, normal, tight, vtight
89
90       -gfn1
91           Use GFN1-xTB.
92
93       -gfn2
94           Use GFN2-xTB. [default]
95
96       -gff, -gfnff
97           Use GFN-FF (requires xtb(1) 6.3 or newer). (For GFN-FF searches
98           bond constraints are applied automatically.)
99
100       -gfn2//gfnff
101           GFN2-xTB//GFN-FF composite mode.
102
103       Adding additional constraints to the calculations:
104
105       The user is able to include additional constraints to ALL xtb(1)
106       calculations that are conducted by CREST.
107
108       -cinp file
109           Read in a file containing the constraints. Constraints have to be
110           in the same format as in xtb(1). (This was done previously via the
111.constrains” file.)
112
113       -cbonds
114           Define automatic bond constraints (set up from topology).
115
116       -nocbonds
117           Turn off -cbonds. (For GFN-FF, mainly. See above.)
118
119       -fc float
120           Define force constant for defined constraints (-cbonds).
121
122   Options for ensemble comparisons
123       -cregen file
124           Use ONLY the CREGEN subroutine to sort a given ensemble file.
125
126       -ewin real
127           Set energy window in kcal/mol. [default: 6.0 kcal/mol]
128
129       -rthr real
130           Set RMSD threshold in Ang. [default: 0.125 Ang]
131
132       -ethr real
133           Set E threshold in kcal/mol. [default: 0.05 kcal/mol]
134
135       -bthr real
136           Set Rot. const. threshold. [default: 0.01 (= 1%)]
137
138       -pthr real
139           Boltzmann population threshold. [default: 0.05 (= 5%)]
140
141       -temp real
142           Set temperature in CREGEN. [default: 298.15 K]
143
144       -prsc
145           Create a scoord.* file for each conformer.
146
147       -nowr
148           Don’t write new ensemble files.
149
150       -eqv,-nmr,-entropy
151           Compare nuclear equivalences (requires rotamers).
152
153       -cluster int
154           PCA and k-Means clustering of sorted ensemble. Works as extenstion
155           to the CREGEN sorting. int is the number of clusters to be formed.
156
157       -notopo
158           Turn off any topology checks in CREGEN.
159
160   Options for the iMTD-GC workflows
161       -cross
162           Do the GC part. [default]
163
164       -nocross
165           Don’t do the GC part.
166
167       -shake int
168           Set SHAKE mode for MD. (0=off, 1=H-only, 2=all bonds) [default: 2]
169
170       -tstep int
171           Set MD time step in fs. [default: 5 fs]
172
173       -mdlen/-len real
174           Set MD length (all MTDs) in ps. Also possible are multiplicative
175           factors for the default MD length with “xreal”.
176
177       -mddump int
178           xyz dumpstep to Trajectory in fs. [default: 100 fs]
179
180       -vbdump real
181           Set Vbias dump frequency in ps. [default: 1.0 ps]
182
183       -tnmd real
184           Set temperature for additional normal MDs. [default: 400 K]
185
186       -norotmd
187           Don’t do the regular MDs after the second multilevel optimization
188           step.
189
190       -quick
191           Perform a search with reduced settings for a crude ensemble.
192
193       -squick
194           Perform a even further reduced search.
195
196       -mquick
197           Perform a search with maximum reduced settings. (Do not reduce the
198           settings more than that.)
199
200       -origin
201           Track the step of generation for each conformer/rotamer. [default]
202
203       -keepdir
204           Keep sub-directories of the conformer generation step.
205
206       -nci
207           Generate an ellipsoide potential around the input structure and add
208           it to the MTD simulation. This can be used to find aggregates of
209           NCI complexes.
210
211       -wscal real
212           Scale the ellipsoide potential axes by factor real.
213
214   Thermostatistical options (used in entropy mode)
215       -trange lower upper step
216           Entropies are calculated for different temperatures. These are
217           calculated in a temperature range from lower to upper with step in
218           between. [default: 280K-380K in 10K steps]
219
220       -fscal float
221           Frequency scaling factor. [default: 1.0]
222
223       -sthr float
224           Vibrational/rotational entropy interpolation threshold (tau).
225           [default: 25.0 cm^-1]
226
227       -ithr float
228           Imaginary mode inversion cutoff. [default: -50.0 cm^-1]
229
230       -ptot float
231           Sum of population for structures considered in msRRHO average.
232           [default: 0.9 (= 90%)]
233
234   Other tools for standalone use
235       -zsort
236           Use only the zsort subroutine to sort the z-matrix of the input
237           coordinate file.
238
239       -mdopt file
240           Optimize along trajectory or ensemble file in the XYZ format. Each
241           point on the file is optimized.
242
243       -screen file
244           Optimize along ensemble file in the XYZ format. A multilevel
245           optimization is performed with continiously increasing thresholds.
246           After each step the ensemble file is sorted.
247
248       -protonate
249           Find a molecule’s protomes by using a LMO pi- or LP-center
250           approach.
251
252       -deprotonate
253           Find a molecule’s deprotomers.
254
255       -tautomerize
256           Combine the protonation and deprotonation to find prototropic
257           tautomers.
258
259           -trev
260               Do first the deprotonation and then the protonation in the
261               -tautomerize mode, i.e., reverse of the default procedure.
262
263           -iter int
264               Set number of protonation/deprotonation cycles in the
265               tautomerization script. [default: 2]
266
267       -compare f1 f2
268           Compare two ensembles f1 and f2. Both ensembles must have the same
269           order of atoms of the molecule and should contain rotamers.
270
271           -maxcomp int
272               Select the lowest int conformers out of each ensemble to be
273               compared with “-compare”. [default: 10]
274
275       -testtopo file
276           Analyze some stuctural info (topology) for a given file.
277
278       -constrain atoms
279           Write example file “.xcontrol.sample” for constraints in crest.
280           (See -cinp option above.)
281
282       -thermo file
283           Calculate thermo data for given structure. Also requires
284           vibrational frequencies in the TM format, saved as file called
285vibspectrum”.
286
287       -rmsd,-rmsdheavy file1 file2
288           Calculate RMSD or heavy atom RMSD between two structures. Input
289           coords are automatically transformed to Angstroem.
290
291       -splitfile file [from] [to]
292           Split an ensemble from file into seperate directories for each
293           structure. from and to can be used to select specific structures
294           from the file. The new directories are collected in the SPLIT
295           directory.
296

NOTES

298       View literature references with --cite.
299

AUTHORS

301       P.Pracht
302
303       S.Grimme
304
305       Universitaet Bonn, MCTC
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309Crest 2.11.0                      2022-05-24                          CREST(1)
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