[gmx-users] Protein-Ligand complex MD

Adamu, Aliyu aliyu.adamu.12 at aberdeen.ac.uk
Thu Feb 25 05:39:24 CET 2016


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

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