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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:
<blockquote cite="mid:4ACD1387.3020702@anu.edu.au" type="cite">Arik
Cohen wrote:
<br>
<blockquote type="cite">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.
<br>
</blockquote>
<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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