I'm running a protein-ligand Molecular Dynamic Simulation but getting the following error after hitting mdrun. Can anyone offer a solution to this? Thanks in advance.
Fatal error:
66 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.
Unstable system. Available solutions include, for instance, using smaller time steps, performing more minimizations, trying another initial configuraitons, choosing another force field, and so on.
Dear Ishtiaque Ahammad
This error usually happens when the system is unstable. Please check this link:
https://manual.gromacs.org/current/user-guide/run-time-errors.html#x-particles-communicated-to-pme-node-y-are-more-than-a-cell-length-out-of-the-domain-decomposition-cell-of-their-charge-group
best
Felippe
Hi Ishtiaque! Your system is not well equilibrated. In order to equilibrate it you shall probably decrease the number of cores. Also it might be useful to revise your cut-off value in the mdp-file if it is possible.
Unstable system. Available solutions include, for instance, using smaller time steps, performing more minimizations, trying another initial configuraitons, choosing another force field, and so on.
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