[gmx-users] restart a stopped simulation after a power failure? correct command

Justin Lemkul jalemkul at vt.edu
Tue Apr 18 14:22:06 CEST 2017

On 4/18/17 1:21 AM, Adarsh V. K. wrote:
> Dear all,
> I use Gromacs 5.1.4 for protein ligand simulation. How can I restart a
> stopped simulation after a power failure?
> I used the following command to restart the stopped simulation at 6.5 ns.
> *mdrun -s md.tpr -cpi state.cpt*
> Even Though the simulation appeared to be restarted successfully and
> completed required 8.0 ns, the data analysis showed that the simulation was
> stopped at 6.5ns...!!!. ( Not re-started from 6.5 ns and continued till 8.0
> ns.)

What does gmx check tell you about your files, e.g. how many frames does it find 
in the trajectory?  Does the .log file or stderr/stdout give any clues about how 
appending was treated?



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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