GROMACS version: 2023.3
GROMACS modification: No
Hello everyone,
I have generated the model of my protein in the membrane (5 POPC:2 POPE:2 CHOL) using CHARMM-GUI. In particular, I generated the WT protein and a mutant (where a point mutation was introduced with CHARMM-GUI).
The forcefield chosen is CHARMM36 and the box is about 360,000 atoms big. While the WT simulations are running fine on the cluster of my institute, the mutant simulations stop after a few minutes into the production run.
Here is the error I get from the log:
“var/lib/slurm/slurmd/job00217/slurm_script: line 83: 51383 Segmentation fault (core dumped) /storage/software/gromacs/2023.3/gromacs/bin/gmx mdrun -v -deffnm ${istep} -ntmpi 4 -ntomp 16 -gpu_id 0,1,2,3 -nb gpu -pme gpu -npme 1 -pmefft gpu -bonded gpu -update gpu -pin on”
I am not sure if the issue lies with the mutant system itself, the input files, or something else in my workflow.
I have attached the relevant .mdp files and the .tpr file for your reference.
tpr file: Gromacs
step7_production.mdp (1.1 KB)
Vittoria
could you please provide the full log file and the output from the cluster.
it looks like issue with job submission/cluster related.
Sure. I can’t see any issue in the log file while the cluster output reports the error I wrote in the question.
slurm-159.out.txt (227.3 KB)
step7_1.log (215.0 KB)
could you please try resubmit by
gmx mdrun -v -deffnm step7_1 -gpu_id 0123 or (-gpu_id 0 only) -nb gpu -bonded gpu -nb gpu.
and update the status here
I resubmitted the job using the following command:
gmx mdrun -v -deffnm step7_1 -ntmpi 4 -ntomp 16 -gpu_id 0123 -nb gpu -bonded gpu
I finally got a more informative error message:
Fatal error:
2 particles communicated to PME rank 2 are more than 2/3 times the cut-off out
of the domain decomposition cell of their charge group in dimension x.
This usually means that your system is not well equilibrated.
I am attaching the log files.
slurm-224.out.txt (943.6 KB)
step7_1.log (134.1 KB)
you can visit here and see what is the issue
https://manual.gromacs.org/current/user-guide/run-time-errors.html
either system is not well minimised or equilibrated or something wrong with your cooridnates. how you built the system
Hi @vittoriananna
Have you now resolved the segmentation fault