Greetings,
I am trying to run GROMACS 2020.3 on a supercomputer using this command to do the production run:
mpirun -np 24 gmx_mpi mdrun -v -s AB_md_0_1.tpr -deffnm AB_md_0_1 > AB_md_1.log
however, it produces this error for each core used:
Fatal error:
525 particles communicated to PME rank 3 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.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
How can I solve this error? should I equilibrate it more?
attached are the log file produced from the run and the slurm file containing the errors.
Thanks
Dear Ibrahim, you should equilibrate more and with different techniques. Good luck
Dear Ibrahim,
I had the same problems like you. I solved it by using following way: at first, I equilibrate the system (NVT, NPT) in my local computer for couple of nano seconds (e.g., 10, 50 or max 100 ns), then I submitted to HPC. This is how I solved my problems. Is it possible to equilibrate your system in your local machine instead of supercomputer first? If yes then do it .After that you can submit the job in your supercomputer for full equilibration with different techniques (according to Prof. Andre Silva Pimentel suggestion). I think your problem will be solved. Best of luck.
Hi Ibrahim! Try to decrease the number of cores after mpirun and equilibrate on the smaller number of cores. Then for production run you may recompile it and run on the larger number of cores.
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