[gmx-users] protein-ligand complex fatal error

Justin Lemkul jalemkul at vt.edu
Mon Dec 8 23:42:31 CET 2014

On 12/8/14 2:36 PM, Yaser Hosseini wrote:
> hi gromacs users
> i want to run  Protein-Ligand Complex but when i want to run this command :
> mdrun -deffnm nvt
> i got this error
> Fatal error:
> 4 particles communicated to PME node 2 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.
> what can i do for fix it???


You need to tell us everything you've done to build and prepare the system, 
including ligand topology, outcome of EM, etc. if you want any sort of useful 



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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