[gmx-users] Extending simulation problem.

[Mark Abraham]

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
>> 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 line.

... And falling back on the contents of the .tpr to start at the designated
start time, if there's no checkpoint provided.

Mark

>
> -Justin
>
> --
> ==================================================
>
> 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
> http://mackerell.umaryland.edu/~jalemkul
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