Lost particles while sorting Gromacs 2016.4
Software Inconsistency Error:
Lost particles while sorting (6 out of 8)
Happens during NPT equilibration on 16 processors of standard GPUs. Affected version is 2016.4. The job however runs on an older gromacs 5.1.0 (double precision)without any hitches. Another thing to note is that after the NPT step (run with 5.1.0) is over if one creates a new run.tpr file for the production run using the 2016.4 version it runs fine. The production simulation runs fine on the native gromacs 5.1.0 version as well. It seems like the NPT step is getting screwed up in 2016.4. The system consists of a membrane protein in detergent micelle having a total number of atoms ~ 88747.
#2 Updated by Mark Abraham about 2 years ago
My general suggestion to you is that pressure coupling with parrinello-rahmann is known to be unstable when the volume has a significant change - thus might work or not with different versions or inputs arbitrarily. Does that apply in your case? What happens if you follow general practice and correct the volume with berendsen pressure coupling first?
#3 Updated by Berk Hess about 2 years ago
- Status changed from New to Rejected
You are running Parrinello-Rahman pressure coupling together with position restraints. This is very likely the source of instability. You should not use Parrinello-Rahman for equilibration and certainly not combined with position restraints.
Please try this with Berendsen pressure coupling instead. I am marking this issue as rejected, but please reply when it also fails with Berendsen.
We could consider adding a grompp warning when combining position restraints with Parrinello-Rahman, but I could imagine valid uses. A note is another option.
Another issue is that we get a software inconsistency error instead of a nice error message. But that is often difficult to avoid with an exploding system.