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

[Justin Lemkul]

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.

-Justin

>
> 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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>
>
>

-- 
==================================================

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

==================================================