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

[rajat desikan]

I guess, the more important question is whether the checkpoint file stores
the previous checkpoints as well. If it stores only the last checkpoint at
20 ns, then I guess there is no way to rerun from 18 ns.

I do not store a .trr because of space constraints and hence I do not have
the velocities. otherwise, I would have used the snapshot from 18ns and
extended the simulation. Now, it looks like I will have to re-generate the
velocities and re-equilibrate the system.


On Mon, Jul 15, 2013 at 6:22 PM, rajat desikan <rajatdesikan at gmail.com>wrote:

> 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
>>
>> --
>> ==============================**====================
>>
>> 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
>>
>> ==============================**====================
>>
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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
>



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