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

[Justin Lemkul]

On 7/15/13 8:56 AM, rajat desikan wrote:
> 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.
>

It does not.  Checkpoints are recycled every -cpt minutes.  You can keep all 
checkpoints by using the mdrun -cpnum option, but I suspect that will use up a 
lot of disk space.

> 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.
>

Or just re-run the simulation from the same .tpr file you used before.

-Justin

>
> 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
>>
>
>
>

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

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

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