On 8/11/13 9:16 AM, Joshua Adelman wrote:
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.
There is no need to truncate anything. If you're concatenating later with
trjcat, they will be stitched together properly with frames from the second
trajectory overwriting the frames in the first (i.e. the stretch in run_002.trr
that is "past" the checkpoint will be re-calculated in run_003.trr and
incorporated seamlessly). The trjcat documentation alludes to this behavior.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
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