crest-lab / crest

CREST - A program for the automated exploration of low-energy molecular chemical space.
https://crest-lab.github.io/crest-docs/
GNU Lesser General Public License v3.0
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-hflip flag not detected #157

Closed AndrewPuente closed 8 months ago

AndrewPuente commented 1 year ago

My compound has several -OH groups and I wanted to add the -OH sampling enhancement to a CREST conformational search. I checked the settings with a dry run (below) and the -hflip or -noflip flag does not seem to be recognized. Just checking that adding the -hflip does engage the appropriate subroutine. I have performed a dry run with both the conda pre-compiled binaries (below) and ones compiled from source code (not included).

 Command line input:
 > crest crest_best.xyz --gfn2 --alpb dmso --hflip --dry

  -gfn2 : Use of GFN2-xTB requested.
  --alpb dmso : implicit solvation

******************************************************************************************
**                                  D R Y    R U N                                      **
******************************************************************************************
 Dry run was requested.
 Running CREST with the chosen cmd arguments will result in the following settings:

 Input file : coord

 Job type :
  1.  Conformational search via the iMTD-GC algo

 Job settings
  sort Z-matrix        :      F

 CRE settings
  energy window         (-ewin) :    6.0000
  RMSD threshold        (-rthr) :    0.1250
  energy threshold      (-ethr) :    0.0500
  rot. const. threshold (-bthr) :      0.01
  T (for boltz. weight) (-temp) :    298.15

 General MD/MTD settings
  simulation length [ps]    (-len) : <system dependent>
  time step [fs]          (-tstep) :       5.0
  shake mode              (-shake) :         2
  MTD temperature [K]    (-mdtemp) :    300.00
  trj dump step  [fs]    (-mddump) :       100
  MTD Vbias dump [ps]    (-vbdump) :       1.0

 XTB settings
  binary name        (-xnam) : xtb
    binary: "xtb"
    status: present
    path  : /home/plpgroup/anaconda3/envs/xtb/bin/xtb
  GFN method         (-gfn)  : --gfn2
  (final) opt level  (-opt)  : 2
  Implicit solvation (-alpb) : dmso
pprcht commented 1 year ago

Hi, apparently the flag is missing in the dry run output, thanks for pointing that out. However, it is detected by the program. In fact, the routine is called by default after the metadynamics if -XH groups are present. Look for the Additional orientation sampling header

AndrewPuente commented 1 year ago

Awesome! Thank you!

AndrewPuente commented 1 year ago

Just following up. Without calling the -hflip flag explicitly, I do see the Additional orientation sampling during a conformation search with implicit solvent. I do not see the header when performing QCG without structure crossing. Is it recommended to not add the subroutine unless you believe the additional sampling is necessary in a QCG run?

cplett commented 1 year ago

Hi, I actually never tested the influence of the -hflip on a QCG run, but I would only use the flag if it is expected that additional sampling is necessary.

github-actions[bot] commented 8 months ago

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