[gmx-users] Snapshots in different files

[Mark Abraham]

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