On 14/02/2012 11:39 PM, Ehud Schreiber wrote:
Dear Mark (or anybody else interested),
The .trr file does include the final (t = 217) frame - first, trjconv
said:
Reading frame 3 time 217.000
and second this is verified by converting the whole trajectory to .gro:
trjconv -f 1IARcompleted_WT_minimized.trr -s
1IARcompleted_WT_minimized.tpr -o 1IARcompleted_WT_minimized_path.gro
It therefore seems the behavior is a bug, as the last frame is there,
and is needed, especially in minimizations. An output in a .gro format
is not sufficient for a further minimization because of its limited
accuracy format of coordinates.
I looked at the code. This is an artefact of trjconv having to try to
work out the spacing of the frames in your .trr to then work out which
frame is probably going to be the closest. It assumes the frame will be
equally spaced, and accepts the first frame that is closer than half the
spacing it computes from the first two frames. Since your frames are
presumably 100, 200 and 217, the "spacing" is 100 and it accepts 200
because it's the first one it finds within 100/2 of 217.
You can work around this in lots of ways (trjconv -b 217; using
nstxout=0 in the first EM; using nstxout=1 in the first EM; using
nstxout extremely large in the first EM; taking the EM output .trr and
giving it to the next grompp -t without doing anything).
Also, my mdrun did not produce a checkpoint file (I'm not sure whether
because I didn't ask to or because the run was shorter than 15 minutes).
OK, maybe EM has a different behaviour (no checkpoint, thus write last
configuration always).
Mark
Thanks,
Ehud Schreiber.
------------------------------
Message: 2
Date: Tue, 14 Feb 2012 21:58:10 +1100
From: Mark Abraham<[email protected]>>
Subject: Re: [gmx-users] FW: trjconv -dump problem
To: Discussion list for GROMACS users<[email protected]>>
Message-ID:<[email protected]>>
Content-Type: text/plain; charset="iso-8859-1"
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"
0.000000 -31997.519531
0.000000 -33810.406250
200.000000 -69850.609375
217.000000 -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
------------------------------------------------------
.
.
-dump time 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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