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.
Any way thanks again
Arik
Dallas B. Warren wrote:
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.)
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.
Catch ya,
Dr. Dallas Warren
Department of Pharmaceutical Biology
Pharmacy and Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.war...@pharm.monash.edu.au
+61 3 9903 9167
---------------------------------
When the only tool you own is a hammer, every problem begins to
resemble a nail.
*From:* gmx-users-boun...@gromacs.org
[mailto:gmx-users-boun...@gromacs.org] *On Behalf Of *Arik Cohen
*Sent:* Thursday, 8 October 2009 9:27 AM
*To:* Discussion list for GROMACS users
*Subject:* Re: [gmx-users] Snapshots in different files
Thanks for answering.
This would not be the case so much since another program(sniffer) can
be working along side gromacs
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.
The aim here is to do an MD from which an ensemble of the C-alpha will
be created.
Thanks again
Arik
Mark Abraham wrote:
Arik Cohen wrote:
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.
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.
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.
Why do you even want separate PDB frames? Visualization tools like VMD
will read the trajectory files.
Mark
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