[gmx-users] RE: trjconv -dump problem
schreib at compugen.co.il
Tue Feb 14 13:39:30 CET 2012
Dear Mark (or anybody else interested),
The .trr file does include the final (t = 217) frame - first, trjconv
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.
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).
> Message: 2
> Date: Tue, 14 Feb 2012 21:58:10 +1100
> From: Mark Abraham <Mark.Abraham at anu.edu.au>>
> Subject: Re: [gmx-users] FW: trjconv -dump problem
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>>
> Message-ID: <4F3A3E42.6000605 at anu.edu.au>>
> 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.
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