[gmx-users] Fwd: segmentation fault on gpus

Justin Lemkul jalemkul at vt.edu
Tue Jun 24 03:04:45 CEST 2014

On 6/23/14, 5:53 PM, ram bio wrote:
> Dear Gromacs Users,
> I have been trying to simulate protein-ligand complex using gromacs
> versions that use verlet cutoff scheme on gpus.
> These are some of the issues that i could resolve, and any kind of
> suggestion or help is appreciated.
> 1. With gromacs 4.6.5 i could simulate crystal structure from pdb but not
> modelled protein with ligand always ended up in segmentation fault. The MD
> run during equillibration runs for gew thousands of steps and errors out as
> segmentation fault, so i have to rerun using previous cpt file, for a run
> of 2ns to complete i have to rerun it for 7-10 times.
> So if the the system id not minimized, why would it go into rerun?
> 2. I though it could be a bug and used 4.6.3 and 5.0 release, with this
> trial i could equillibrate just modelled protein but not with the
> protein-ligand complex. The same error occurs as i mentioned above with
> protein-ligand complex...
> I am attaching my mdp file and the minimized structure that i am using for
> equillibration.

The list doesn't accept attachments.

It seems clear to me that your ligand topology is not stable.  If the protein 
works, but the protein+ligand doesn't, what's changing?  That's the likeliest 
source of your problem.



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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

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


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