[gmx-users] Extending simulation problem.
mark.j.abraham at gmail.com
Fri Aug 22 16:21:19 CEST 2014
On Aug 22, 2014 2:51 PM, "Justin Lemkul" <jalemkul at vt.edu> wrote:
> 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
>> time 0.000 and length 100000.000
>> 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 line.
... And falling back on the contents of the .tpr to start at the designated
start time, if there's no checkpoint provided.
> 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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