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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