[gmx-users] Multiple writing to same trajectory issue

Matthias Ernst matthias.ernst at physik.uni-freiburg.de
Thu Oct 16 17:04:11 CEST 2014

Dear users,

I usually resume calculation of a trajectory from a checkpoint file
appending to the old files (which, as I learned, is obviously not a good
Due to some issue with our queueing system, several jobs that were
marked as depending on each other started at once and all wrote at the
same trajectory file. I noticed this only 10 hours later.

What does Gromacs do if a time frame is written to a trajectory that
already has this time? Is it doubled or discarded? And the same for the
other files (log/edr...)?

I think using trjconv with -e option just until the timestep of the
multiple writing should recover at least the data gained until then, but
is there a possibility to recover and resume my run at that point?

Thanks for your help,

Progress... http://www.phdcomics.com/comics/archive.php?comicid=1611

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