[gmx-users] Using the checkpoint file to restore corrupt trajectory.
jalemkul at vt.edu
Mon Jul 15 14:56:00 CEST 2013
On 7/15/13 8:52 AM, rajat desikan wrote:
> Hi Justin,
> The checkpoint file has gone on to 20 ns. If I do a rerun, the simulation
> will finish in one step.
You need a checkpoint file that corresponds to a good frame before the
corruption. If you don't have that, you can't fix the broken trajectory. Your
first message implied that you had a good frame. Since that's not the case,
you'll have to either re-run the simulation or skip the bad frame and settle for
fewer data points.
> On Mon, Jul 15, 2013 at 6:11 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>> On 7/15/13 8:38 AM, Rajat Desikan wrote:
>>> I have a 20 ns long trajectory which has become corrupted beyond 18ns. I
>>> have the full checkpoint file. Is there any way I can use mdrun and the
>>> to rerun the simulation from 18ns and append it to the current .xtc
>>> (After I
>>> have clipped the part beyond 18ns by trjconv)? I did not find the
>>> appropriate flag in the mdrun online manual pages.
>> It's no different than doing any restart.
>> mdrun -s topol.tpr -cpi good_state.cpt -noappend
>> Then concatenate trajectory and energy files with trjcat and eneconv.
>> Justin A. Lemkul, Ph.D.
>> Postdoctoral Associate
>> 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 <jalemkul at outerbanks.umaryland.edu> |
>> (410) 706-7441
>> gmx-users mailing list gmx-users at gromacs.org
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Justin A. Lemkul, Ph.D.
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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