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On 14/02/2012 7:59 PM, Ehud Schreiber wrote:
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<p class="MsoNormal">Dear Gromacs users,<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">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:<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">.<o:p></o:p></p>
<p class="MsoNormal">.<o:p></o:p></p>
<p class="MsoNormal">@ title "Gromacs Energies"<o:p></o:p></p>
<p class="MsoNormal">@ xaxis label "Time (ps)"<o:p></o:p></p>
<p class="MsoNormal">@ yaxis label "(kJ/mol)" <o:p></o:p></p>
<p class="MsoNormal">.<o:p></o:p></p>
<p class="MsoNormal">.<o:p></o:p></p>
<p class="MsoNormal">@ s0 legend "Potential"<o:p></o:p></p>
<p class="MsoNormal"> 0.000000 -31997.519531<o:p></o:p></p>
<p class="MsoNormal"> 0.000000 -33810.406250<o:p></o:p></p>
<p class="MsoNormal"> 200.000000 -69850.609375<o:p></o:p></p>
<p class="MsoNormal"> 217.000000 -69898.031250<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">I wanted to extract only this last frame
from the .trr file, so used<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">trjconv -f 1IARcompleted_WT_minimized.trr
-o 1IARcompleted_WT_minimized_217.trr -dump 217<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">However, this seems to have produced a file
with the t = 200 ps conformation, though the dump parameter
was recorded, as trjconv output was:<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">.<o:p></o:p></p>
<p class="MsoNormal">.<o:p></o:p></p>
<p class="MsoNormal">Option Type Value Description<o:p></o:p></p>
<p class="MsoNormal">------------------------------------------------------<o:p></o:p></p>
<p class="MsoNormal">.<o:p></o:p></p>
<p class="MsoNormal">.<o:p></o:p></p>
<p class="MsoNormal">-dump time 217 Dump frame
nearest specified time (ps)<o:p></o:p></p>
<p class="MsoNormal">.<o:p></o:p></p>
<p class="MsoNormal">.<o:p></o:p></p>
<p class="MsoNormal">Will write trr: Trajectory in portable xdr
format<o:p></o:p></p>
<p class="MsoNormal">trn version: GMX_trn_file (single
precision)<o:p></o:p></p>
<p class="MsoNormal">Reading frame 2 time 200.000 <o:p></o:p></p>
<p class="MsoNormal">Dumping frame at t= 200 ps<o:p></o:p></p>
<p class="MsoNormal">Reading frame 3 time 217.000 <o:p></o:p></p>
<p class="MsoNormal">.<o:p></o:p></p>
<p class="MsoNormal">.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Also, using -dump 200 gave an identical
file to the above.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Any idea why the expected timeframe isn’t
reproduced?<o:p></o:p></p>
<p class="MsoNormal">I’m using gromacs 4.5.3.</p>
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<br>
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.<br>
<br>
Mark<br>
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