[gmx-users] Error in MD Simulation...

Justin Lemkul jalemkul at vt.edu
Sat Feb 15 14:42:22 CET 2014

On 2/15/14, 4:12 AM, Kalyanashis wrote:
> I have submitted a job for PR MD simulation but I got an error  "Program
> mdrun, VERSION 4.6.3
> Source code file: /compile/gromacs-4.6.3/src/gmxlib/checkpoint.c, line: 1619
> File input/output error:
> Cannot rename checkpoint file; maybe you are out of disk space?
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors"
> But now free disk space in our cluster is around 60% i.e. 2 TB free space is
> there.
> I submitted this job for 3 time and got same error and it was submitted for
> 1 ns simulation but 1st time it was terminated after 232 ps, 2nd time after
> 358 ps and 3rd time at 688 ps.
> Can please tell me what is the problem and please suggest me a probable
> solution.

The simulation is probably crashing.  Check the .log file and stderr/stdout.



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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