[gmx-users] em and nvt problem

[Kashif]

Hi
Whenever I tried to simulate one of my docked complex, the energy
minimization step converged very fast and complete at 112 steps. And when I
proceed with NVT equilibration I got split structures like ........
step4b_n6.pdb
step4c_n6.pdb
step5b_n6.pdb
step5c_n6.pdb

I have already docked the drug with my protein using different tool in
order to get different docked pose of drug. So that I could get different
topology file and coordinate file of the drug from PRODRG server.
But the same problem encounters.
Some time I got the error like .........

Fatal error:
1 particles communicated to PME node 5 are more than 2/3 times the cut-off
out of the domain decomposition cell of their charge group in dimension y.
This usually means that your system is not well equilibrated.
........................................................

kindly help

regards
kashif