[gmx-users] system blowing up

Justin Lemkul jalemkul at vt.edu
Fri Dec 2 13:48:39 CET 2016

On 12/1/16 1:23 PM, abhisek Mondal wrote:
> Hi,
> I'm constantly getting a strange error of system blow up during
> equilibration procedure. I'm relatively new to gromacs, please help me to
> get my things straight.
> I have a ligand bound protein structure in solvated condition.
> So, I was using:
> gmx mdrun -v -deffnm em #for minimization
> Upon successful completion, I try to equilibrate using:
> gmx mdrun -deffnm npt
> But this command is failing with a lot of LINCS errors.
> Surprising thing is that, I'm running the same code in 2 clusters
> simultaneously. In one cluster it is running fine but in other cluster it
> is giving me LINCS error.
> Can you please suggest what actually is going wrong.




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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