On 14/02/2012 7:59 PM, Ehud Schreiber wrote:
Dear Gromacs users,
I minimized a protein structure 1IARcompleted_WT.pdb, getting, among
others, the files 1IARcompleted_WT_minimized.trr and
1IARcompleted_WT_minimized_potential_energy.xvg . Looking at the
latter file showed the last frame to be at 217 ps:
.
.
@title "Gromacs Energies"
@xaxis label "Time (ps)"
@yaxis label "(kJ/mol)"
.
.
@ s0 legend "Potential"
0.00 -31997.519531
0.00 -33810.406250
200.00 -69850.609375
217.00 -69898.031250
I wanted to extract only this last frame from the .trr file, so used
trjconv -f 1IARcompleted_WT_minimized.trr -o
1IARcompleted_WT_minimized_217.trr -dump 217
However, this seems to have produced a file with the t = 200 ps
conformation, though the dump parameter was recorded, as trjconv
output was:
.
.
Option Type Value Description
--
.
.
-dumptime 217 Dump frame nearest specified time (ps)
.
.
Will write trr: Trajectory in portable xdr format
trn version: GMX_trn_file (single precision)
Reading frame 2 time 200.000
Dumping frame at t= 200 ps
Reading frame 3 time 217.000
.
.
Also, using -dump 200 gave an identical file to the above.
Any idea why the expected timeframe isn't reproduced?
I'm using gromacs 4.5.3.
Your nstxout parameter means not every frame is written. Prior to the
implementation of checkpointing, the final frame was written to the .trr
regardless of nstxout, but that no longer occurs. The final frame is in
your checkpoint file, and you can use that anywhere you might use a
coordinate file - including trjconv to get a simple coordinate file from it.
Mark
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