GROMACS version:2018.1
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Hello everyone,
I’m trying to optimize a cluster for the best performance. I have used a .tpr file, which was simulated for 1 microsecond in another system. Now, when I run the .tpr in the current HPC, I’m getting an error as follows:
Fatal error:
88 particles communicated to PME rank 4 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 have changed node 4 to 1 and altered other parameters in the SLURM script:
#SBATCH --nodes=1
#SBATCH --ntasks=6
#SBATCH --tasks-per-node=6
Now, I have created the simulation system from the HPC with the same structure and minimized to a maximum force of <1000, and the simulation is equilibrated—all these on a single node. However, when I run the simulation without the SLURM script, on the single node, it runs without any issue. Nonetheless, even for a single node, the issue persists when I run it through SLURM.
Can someone have a look at this and provide any suggestions?
The relevant part of the SLURM script and log file is here:
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