I recently had a simulation crash where my .trr and .xtc files extend beyond the last checkpoint time (I'm using 4.6.3). Explicitly something like run_002.trr was written after state.cpt. I was wondering if there was a recommended protocol for truncating run_002.trr such that when I restart from the checkpoint, starting the next trajectory file in the series, run_003.trr will be continuous with the previous one? This is important in terms of going back and treating the series of trajectory files as continuous for analysis purposes.
My preliminary thought is to get the timestamp, T, of the state.cpt file using gmxcheck, and then do `trjconv -f run_002.trr -trunc T`. This seems to work (although I need to check if the coordinates in the truncated file match with the state.cpt file). When I try the same thing with my .xtc file, I get an error message: Fatal error: run_002.xtc is not a trajectory file, exiting This seems strange since running gmxcheck on the xtc file doesn't report any issues. Any suggestions on the proper way to clean up the files or the error message would be appreciated. Best wishes, Josh -- View this message in context: http://gromacs.5086.x6.nabble.com/Cleaning-up-trajectory-files-after-crash-tp5010438.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
