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

[rajat desikan]

Thank you!


On Mon, Jul 15, 2013 at 6:29 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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 <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 <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