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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