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Thanks for replaying. Indeed thats what i did with the BALL library
which was inefficient. This led me eventually to change the library by
adding a feature to it.<br>
<br>
Any way thanks again <br>
<br>
Arik<br>
<br>
Dallas B. Warren wrote:
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<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">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: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">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: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"> <o:p></o:p></span></p>
<div>
<p class="MsoNormal"><span
style="font-size: 10pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">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>
<a class="moz-txt-link-abbreviated" href="mailto:dallas.warren@pharm.monash.edu.au">dallas.warren@pharm.monash.edu.au</a><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: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">
<o:p></o:p></span></p>
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<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
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<p class="MsoNormal"><b><span
style="font-size: 10pt; font-family: "Tahoma","sans-serif"; color: windowtext;">From:</span></b><span
style="font-size: 10pt; font-family: "Tahoma","sans-serif"; color: windowtext;">
<a class="moz-txt-link-abbreviated" href="mailto:gmx-users-bounces@gromacs.org">gmx-users-bounces@gromacs.org</a>
[<a class="moz-txt-link-freetext" href="mailto:gmx-users-bounces@gromacs.org">mailto:gmx-users-bounces@gromacs.org</a>] <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>
</div>
</div>
<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>
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