[gmx-users] restarting MD after error in the middle of trajectory

[Tomek Wlodarski]

Thanks Justin.

Yes, trajectory was corrupted but I did not get any error message during
the run, only when I started to analyse trajectory.
Is there a way to know immediately, during simulation, when trajectory gets
corrupted instead of after use of gmxcheck?
Thanks.

tomek



On Wed, Jan 8, 2014 at 2:17 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 1/7/14, 11:34 AM, didymos wrote:
>
>> Hi,
>>
>> I have strange situation.
>> I am running MD with 4 replicas and when I recently checked the trajectory
>> with gmxcheck in one replica I got this error:
>>
>> Fatal error:
>> Magic Number Error in XTC file (read 0, should be 1995)
>>
>>
> That usually means the trajectory was corrupted.
>
>
>
>> It is arround 50ns of the simulation, and right now I have 120ns.
>> I would like to restart my simulation from the part before 50ns but I am
>> not
>> sure how to do this because my cpt file are written after 120ns...
>> Can I generate new cpt file based on the part of the simulation before
>> 50ns?
>>
>
> Unless you have saved all of them (mdrun -cpnum), which is not the default
> behavior, the previous states are lost as checkpoint files are recycled.
>  You could, in theory, extract matching time frames from an .edr and .trr
> file and do an old-style restart from those frames, i.e.
> http://www.gromacs.org/Documentation/How-tos/
> Extending_Simulations#Version_3.3.3_and_Before.  You will not get exact
> continuation, but the resulting trajectory should be reasonable.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Postdoctoral Fellow
>
> 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
>
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>
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