[gmx-users] 1 particles communicated to PME rank 3 are more than 2/3 times the cut-off out

[Seketoulie Keretsu]

Dear Gromacs Community,

I have come across this problem during NVT equilibration of an all atom
protein-ligand MD simulation.

Fatal error:
1 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 basically used the nvt and npt equilibration approach given in tutorial
by Justin. I have tried changing the equilibration process  by gradually
increasing temperature to 100K. However it still shows the same error. I
have tried with other conformation of ligand as initial structure also but
no improvement. Could you advise how to go about this?

Thank you all.

Sincerely,
Seke