[gmx-users] Protein-Ligand complex MD

[Adamu, Aliyu]

Hello,

I am running the Gromacs tutorial for Protein-Ligand complex described by Justin Lemkul. I am using Gromacs 4.6.7 on ubuntu PC platform. I successfully ran all the commands until the equilibration stage. the 'grompp -f nvt.mdp -c em.gro -p topol.top -n index.ndx -o nvt.tpr' command was successful, but when I tried to run mdrun, it gave this fatal error: 2 particles communicated to PME node 4 are more than 2/3 times the cut-off of the domain decomposition cell of their charge group in dimension x. I repeated several times, but still the error posed up.
Please can any one help me on how to fix this error.

Many thanks
Ali