From: Debasis Sengupta (
Date: Fri Jul 29 2011 - 16:58:34 CDT

I have created a trajectory file which has variable number of atoms in
each frame. VMD appears to be reading only the first frame. My
objective is to follow the environment of certain atoms in the
trajectory. For example, I want follow the environment of atom numbers,
say, i, j and k in entire trajectory file. What I have done is, I
created a secondary trajectory file (wrote a utility code to by reading
the main trajectory file created by the MD program) containing atoms
that are within, say, 3 angstroms from the atoms i, j and k. Is there
any way this can be done within VMD in easier way? I am not familiar
with the VMD scripting. If scripting is the only answer, does anyone
have any such script? Thanks