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

[Mark Abraham]

Yes, it would be horribly slow, and might not even work. A filesystem that
does not flush to disk when we tell it to do so might read it back from the
same buffer even if we were to try to check anything more. There are mdrun
options for keeping things like numbered checkpoint files, if you think you
need them. Scripting some sanity checks in your run scripts can also be
useful.

Mark
On Jan 8, 2014 1:33 PM, "Justin Lemkul" <jalemkul at vt.edu> wrote:

>
>
> On 1/8/14, 6:22 AM, Tomek Wlodarski wrote:
>
>> 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?
>>
>
> No, there is no on-the-fly checking for the integrity of each frame.  That
> would probably be a horrible bottleneck in I/O.  The reasons for the
> corrupted frames are usually external to Gromacs, anyway, like file system
> glitches, network problems, etc.
>
> -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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