From: Axel Kohlmeyer (
Date: Mon Dec 09 2013 - 08:32:15 CST

Possible? Yes.
Automatic? No.

It would require quite a bit of custom vmd scripting. Not very difficult, but you would have to combine different pieces of scripting that have been discussed before.

Dr. Axel Kohlmeyer
International Centre for Theoretical Physics, Trieste. Italy.

-----Original Message-----
From: Ali Alizadeh <>
Date: Mon, 9 Dec 2013 16:39:30
To: Vmd l<>
Subject: vmd-l: Atomic trajectory to COM trajectory,

Dear All users,

I have done an NVT ensemble with LAMMPS package. I have saved its
trajectory in trr format.

Now, I want to convert that atomic trajectory to trajectory of center of
mass of molecules. Is it

possible? Does any body have experience? I want to do this for calculation
of density and g(r)

values of COMs in VMD. Can I save the coordinates of atomic trajectory of
atoms as COM



Ali Alizadeh