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

[rajat desikan]

Hi Justin,
The checkpoint file has gone on to 20 ns. If I do a rerun, the simulation
will finish in one step.


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:
>
>> 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.
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-- 
Rajat Desikan (Ph.D Scholar)
Prof. K. Ganapathy Ayappa's Lab (no 13),
Dept. of Chemical Engineering,
Indian Institute of Science, Bangalore