[gmx-users] Cleaning up trajectory files after crash

Joshua Adelman jla65 at pitt.edu
Sun Aug 11 15:16:35 CEST 2013

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

Any suggestions on the proper way to clean up the files or the error message
would be appreciated.

Best wishes,

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