[gmx-users] simulation explode while switching from NVT to NPT

Justin Lemkul jalemkul at vt.edu
Fri Sep 6 18:52:31 CEST 2013

On 9/6/13 12:48 PM, Golshan Hejazi wrote:
> Dear Rafael,
> Thanks for your reply.
> Yes, I did follow the link. This means that the system is not equilibrated well. I tried to perform some more minimization but it seems that steepest decent have already minimized it well.
> Therefore I decided to perform MD at lower T. I tried 5ns of NVT simulation at 20K and another 5ns at 50K. But still as soon as I turn on the barostate ... the simulation crashes.
> Do you have any other suggestion?

There are numerous things that could be going wrong, but without a full .mdp 
file it's hard to guess.  Further, have you done any validation of your topology 
prior to this run?



Justin A. Lemkul, Ph.D.
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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