I have been working on a protein-ligand complex simulation. While I have been careful all the way in preparing the necessary files including the .top and the .gro files I have come across an error stating "2 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" while running the mdrun. Initial lookout into this issue gave indications of the system getting blown up. I initially tried to troubleshoot the issue by lessening the time steps as suggested in the gromacs documentation but couldn't resolve the issue. Could anybody give suggestions regarding this issue?
Thanks
http://www.gromacs.org/Documentation/Terminology/Blowing_Up
The most likely causes are incorrect .mdp settings or an incorrectly parametrized ligand. Without more details, it's impossible to say.
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