2 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.
I got this error while performing gmx mdrun -deffnm nvt
Any solution for this?
As the error message suggest you need to equilibrate the system.
1) The energy minimization probably did not work very well. Try looking at the maximum force for the minimization.
2) Check you initial configuration using VMD to see everything is fine.
3) If that does not work, try to reduce the timestep and run NVT for a short time and then increase the timestep back to normal and run in again.
4) Check if your total charge of the system is neutral.
There can be other issues depending on what you are doing.
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