Dear gmx'ers,
I've done a long NVE simulation in vacuo. During this run I had to take care to
diminish the total energy drift, so my choice was
comm_mode = None
Now, analysing a smaller subsystem (solute + shell of solvent) I want to
exclude its COM movement. Sorry, I fail to find any instruction how to do it.
Extracting the subset with
trjconv -f traj.trr -s -n my_index.ndx -o subset.trr -center
centers the subsystem well. But as it can be checked with
g_traj -f subset.trr -s subset.tpb -n my_index.ndx -ov -ekt -ekr -com
the velocities in subset.trr remain unchanged.
Ideally I would like, first, to correct the atom velocities to zero COM
velocity, and next to correct them to obtain zero angular momentum of my
subsystem. Could anyone advise me how to correct properly the velocities in
trr-file?
Thank you in advance,
--
Regards,
Dmitri mailto:[email protected]
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