[gmx-users] Extending simulation problem.

Justin Lemkul jalemkul at vt.edu
Fri Aug 22 14:51:29 CEST 2014

On 8/22/14, 8:49 AM, Dawid das wrote:
> Can you just have a quick look at this?
> When I run:
> tpbconv -s npt-md.tpr -extend 95000 -o npt-md.tpr
> to extend simulation by 95 ns this time I got this message at the end:
> Extending remaining runtime of by 95000 ps (now 50000000 steps)
> Writing statusfile with starting step          0 and length   50000000
> steps...
>                                   time      0.000 and length 100000.000 ps
> So it looks like new status file is written and it says that simulation
> will start from the very beginning or did I misunderstand something?
> However when I check state.cpt with gmxdump it looks fine:
> step = 2500000
> t = 5000.000000

All of this is expected.  Using tpbconv doesn't change the start time of the 
.tpr file.  It says "the new .tpr file has a new number of steps" and the 
starting step is determined by the use of a checkpoint file on the mdrun command 



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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