[gmx-users] Extending simulation

Justin Lemkul jalemkul at vt.edu
Wed Oct 14 01:46:12 CEST 2015

On 10/13/15 7:43 PM, thomas knitter wrote:
> Dr. Lemkul,
> My job was terminated. In the log file, it says
> TERM_RUNLIMIT: job killed after reaching LSF run time limit.

You shouldn't be running anything in a queuing system without diagnosing 
problems yourself first.  Based on the scant information you've given, grompp is 
failing (which should take a few seconds), which causes mdrun to fail (again, 
seconds) so nothing in the queue should hang.  But that's irrelevant.  Run 
grompp interactively and see what's causing the problem.



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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