[gmx-users] Corrupted checkpoint file from MD simulation

melichercik at leaf.nh.cas.cz melichercik at leaf.nh.cas.cz
Mon Aug 28 18:21:01 CEST 2017

if you have .trr with saved velocities (at least from time to time), you can create new tpr file starting with the last frame you have.
Command: gmx tpbconv -s <old>.tpr -f <trajectory>.trr -e <energy>.edr -time <from_which_you_want_to_continue> -o <new>.tpr

And with this new .tpr you'll start normal run (gmx mdrun ...) and than you have to concatenate files with gmx eneconv and gmx trjcat. At least the version 4.x required at least the velocities and energies for some frame and I don't think it is possible to continue without them (cause of nature of MD).
Good luck.


On Mon, Aug 28, 2017 at 10:50:09AM -0500, Alexander Yang wrote:
> Hi everyone,
> Recently, I was running a simulation on a computer cluster, but the
> computer cluster unexpectedly crashed. The trajectory file (.xtc) was
> saved, but the checkpoint files (both .cpt and _prev.cpt) seem to be
> corrupted. Does anyone have any recommendations on continuing the
> trajectory despite the corrupted checkpoint files?
> -- 
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