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

jkrieger at mrc-lmb.cam.ac.uk jkrieger at mrc-lmb.cam.ac.uk
Tue Jan 7 18:27:09 CET 2014

Perhaps you should restart without a cpt like you would before version 4.
You could use tpbconv with -time 50000 (ps) to make a new tpr which you
then use with mdrun instead. Hopefully that helps.

Best wishes

> 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)
> 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?
> Thanks for any suggestions.
> Best,
> tomek
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