On 8/11/13 2:33 PM, Joshua Adelman wrote:
On Aug 11, 2013, at 2:12 PM, Justin Lemkul wrote:
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
Hi Justin,
Thanks for your reply. Unfortunately, I was not intending to concatenate the
files, especially in light of the total continuous trajectory taking up a large
amount of disk space. I guess I could just use trjcat on any xtc file where
there was a crash with the subsequent one in the series and use the output
instead, but I'd rather just remove the frames past the checkpoint so that I
can process all of the files without any special checking for this case.
Also, I was looking at the source for gmx_trjconv.c and it looks like the
truncation routine doesn't accept xtc files (although I could be wrong since I
haven't spent much time looking at Gromac's internals):
https://github.com/gromacs/gromacs/blob/d67173b36b78840466e691a4a6657d2b8fdb1c84/src/gromacs/gmxana/gmx_trjconv.c#L463
This does not appear to be documented outside of looking at the source. This
seems particularly confusing because trjconv does take xtc files and the error
message is a little misleading since xtc is a trajectory file, but just not one
of the formats that is allowed with trunc.
Alternatively, I think I could use the `-e` flag to specify the last frame that
I want corresponding to the checkpoint and write to a new file rather than
truncating in-place. Does that sound reasonable?
Yes, using -e would work.
-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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