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

Justin Lemkul jalemkul at vt.edu
Wed Jan 8 13:30:05 CET 2014

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 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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