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<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>If the time frame between snapshots is not too short, you could
have that as the length of each MD run, then simple extend the run to keep on
going. Could be a bit inefficient. (This is how you should run MD anyway, to
ensure don’t lose a lot of information if the computer system you are running
on crashes etc.)<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>I wouldn’t be too surprised if it was possible to hack the code
so that a coordinate file is spat out at some interval (even with a limited
index of atoms). But that is something for those that know the ins and outs of
the code to tell you.<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'> <o:p></o:p></span></p>
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<p class=MsoNormal><span style='font-size:10.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Catch ya,<br>
<br>
Dr. Dallas Warren<br>
Department of Pharmaceutical Biology <br>
Pharmacy and Pharmaceutical Sciences, Monash University<br>
381 Royal Parade, Parkville VIC 3010<br>
dallas.warren@pharm.monash.edu.au<br>
+61 3 9903 9167<br>
---------------------------------<br>
When the only tool you own is a hammer, every problem begins to resemble a
nail.</span><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'> <o:p></o:p></span></p>
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<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
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<p class=MsoNormal><b><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif";
color:windowtext'>From:</span></b><span style='font-size:10.0pt;font-family:
"Tahoma","sans-serif";color:windowtext'> gmx-users-bounces@gromacs.org
[mailto:gmx-users-bounces@gromacs.org] <b>On Behalf Of </b>Arik Cohen<br>
<b>Sent:</b> Thursday, 8 October 2009 9:27 AM<br>
<b>To:</b> Discussion list for GROMACS users<br>
<b>Subject:</b> Re: [gmx-users] Snapshots in different files<o:p></o:p></span></p>
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<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>Thanks for answering. <br>
This would not be the case so much since another program(sniffer) can be
working along side gromacs<br>
examining each snapshot(Max 400 residues == atoms. I'm only interested in the
C-alpha) and then if all criteria are met to extract/or save the coor and
if not to erase the snapshot.<br>
The aim here is to do an MD from which an ensemble of the C-alpha will be
created.<br>
<br>
Thanks again <br>
<br>
Arik<br>
<br>
<br>
<br>
Mark Abraham wrote: <o:p></o:p></p>
<p class=MsoNormal>Arik Cohen wrote: <br>
<br>
<o:p></o:p></p>
<p class=MsoNormal>Thanks allot, but isn't trjconv should be executed after
the trajectory has finished ?. I would like to put each snapshot in a different
file on the fly. <o:p></o:p></p>
<p class=MsoNormal><br>
As Justin said, you can't do that. For starters, it consumes vast amounts of
disk. Also, it doesn't take long to do it after the fact on some workstation,
and it is wasteful to spend your (limited) main compute resources doing I/O
while post-processing output. <br>
<br>
GROMACS workflows are intended to run the simulation fast and efficiently, and
then allow you to process the results with the various tools/filters to extract
the data you need. You can even post-process with mdrun -rerun if you want to
get only a subset of forces or something. The main exception to this principle
is the use of xtc-groups, IIRC. <br>
<br>
Why do you even want separate PDB frames? Visualization tools like VMD will
read the trajectory files. <br>
<br>
Mark <br>
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<o:p></o:p></p>
<pre><o:p> </o:p></pre><pre style='text-align:center'>
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