[gmx-users] how to correct velocities in trajectory file

Dmitri Dubov ddubov at ngs.ru
Thu Jun 17 11:09:20 CEST 2010

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,

 Dmitri                          mailto:ddubov at ngs.ru
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