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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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QCG final geometry optimization at GFN-FF #278

Open moabe84 opened 6 months ago

moabe84 commented 6 months ago

Hi everyone, I'm conducting Solvation Free Energy calculations using QCG for several macromolecules in 100 solvent molecules. I'm curious if it's feasible to employ the GFN-FF method for the Final Geometry Optimization. The default method is GFN2-xTB, which appears to be quite costly for my systems. Here's my command line for the calculations: _crest mol1.xyz --qcg water.xyz --nsolv 100 --gfnff --T 60 --gsolv --nclus 5 --mreset 4 --alpb water --nofix

I'm using CREST version 2.12.

Thanks, Mostafa

cplett commented 6 months ago

Hi Mostafa, after CREST version 2.12, I updated the source code so that the GFN2-xTB optimization was made optionally if a different method should be used and is then only be performed when using the "--fin_opt_gfn2" flag. This feature is currently only available in the Continous release version or an other version compiled with the current source code.

moabe84 commented 6 months ago

Thank you for your reply. If I want to do everything at the GFN-FF level, do I also need to specify the "--enslvl gfnff" keyword: _crest mol1.xyz --qcg water.xyz --nsolv 100 --gfnff --enslvl gfnff --T 60 --gsolv --nclus 5 --mreset 4 --alpb water --nofix

moabe84 commented 6 months ago

I just ran the calculations with the Continous release version (precompiled binaries) using the following command line and it crashed in the "Multilevel Ensemble Optimization" step with this error:

crest pentanol.xyz --qcg benzene.coord --nsolv 25 --gfnff --T 120 --gsolv --nclus 4 --fscal 0.65 --gbsa benzene

_input file name : crest_rotamers_0.xyz output file name : crest_rotamers_1.xyz reference state Etot : -62.1430257400000
forrtl: severe (174): SIGSEGV, segmentation fault occurred Image PC Routine Line Source
crest 0000000002659710 Unknown Unknown Unknown crest 00000000006E1484 cregenconffile 2510 cregen.f90 crest 00000000006C01EC newcregen_ 260 cregen.f90 crest 00000000005AE3A4 confgchk3 913 confscript2_misc.f90 crest 00000000005AE1C8 sort_andcheck 1052 confscript2_misc.f90 crest 0000000000517B0D crestmultilevel 396 search_conformers.f90 crest 0000000000512C61 crest_search_imtd 129 search_conformers.f90 crest 00000000004214E5 qcgensemble 1029 solvtool.f90 crest 0000000000406350 crestsolvtool 102 solvtool.f90 crest 00000000004041F8 MAIN__ 262 crestmain.f90 crest 000000000040336D Unknown Unknown Unknown crest 000000000265B9E0 Unknown Unknown Unknown crest 000000000040324E Unknown Unknown Unknown

cplett commented 3 weeks ago

To apply GFN-FF in every step, both the --gfnff and --enslvl gfnff options need to be used. Thank you for reporting the bug. There have been some bug fixes recently that should also address this issue.

moabe84 commented 3 weeks ago

Thank you for the updates.