[gmx-users] Using the checkpoint file to restore corrupt trajectory.

[Justin Lemkul]

On 7/15/13 8:38 AM, Rajat Desikan wrote:
> Hi,
> 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 .cpt
> 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

-- 
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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 | (410) 706-7441

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