[gmx-users] Protein-Ligand complex MD

Justin Lemkul jalemkul at vt.edu
Thu Feb 25 13:42:08 CET 2016

On 2/24/16 11:39 PM, Adamu, Aliyu wrote:
> 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.

The tutorial system should not crash; it is very robust. You either have 
something wrong in the coordinates or the topology.  Check your work carefully - 
visualize the minimized coordinates, verify that the energy converged nicely, 
check grompp for any warnings that suggest you've put something out of order in 
the topology, etc.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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