Hi,
I got the following error message while running parallelized simulations with OpenMP:
OpenMP threads have been requested with cut-off scheme Group, but these are only supported with cut-off scheme Verlet
I set the cut-off scheme to Verlet by adding the line "cutoff-scheme = Verlet" to my mdp files, as suggested in the mailing list (https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2014-March/088079.html).
However, with this modification to my mdp files, I am still getting the same error message as above.
The Gromacs version I used is 4.6.5, installed via Anaconda.
Thank you for your help in advance!
Kind regards,
Gangtong
Hello Gangtong! To me it looks like you are trying to run with your old tpr-file that is why you get an error with OpenMP threads. It doesn't look like you recompiled it with grompp for the new mdp-file. So you need to run grompp command for the modified mdp-file.
Inna Ermilova
Hi Dr. Ermilova,
Thank you for your reply!
Actually I recompiled the binary tpr files from my new mdp files with grompp when I carried out the simulations.
If I run with "cutoff-scheme=Verlet" using a single CPU thread, the simulations can be done successfully, but in the simulation log files it still showed "cutoff-scheme=Group", as shown in the screenshot attached.
Kind regards,
Gangtong
Hi again! What if you try to write in your mdp-file "coulombtype=cut-off" together with the option "cutoff-scheme=verlet" and then recompile it with grompp?
Hi Dr. Ermilova,
Thank you for your suggestion! I modified the mdp with "coulombtype=cut-off" and also tested with another Gromacs version (2018.3), but the same error message still occurs. In addition, my setting for the VDW type is also "vdwtype=cut-off". I am also trying to identify other possible conflicting options that might overwrite the cut-off scheme with "Group".
Kind Regards, Gangtong
Inna Ermilova
Hello Gangtong,
Set the rvdw value to 1.5, and compile the "cutoff-scheme=verlet" with grompp.
Good Luck !!
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