From: Chaitanya Krishna A (
Date: Mon Jan 02 2006 - 08:01:49 CST

Hi all,

I have the coordinates from an MD run. Now I want to look at an atom and all
the atoms within a certain radius around the chosen atom.

The problem is that in every time step the number of atoms in the sphere is
different and when I give VMD something like the file below, it shows only two
frames and 1 atom in each of the frame.
file :

O 1.0 1.0 1.0

H 0.0 0.0 0.0
H 1.0 1.0 1.0

H 1.0 1.0 1.0
O 2.0 2.0 2.0

But I would like to see 1 atom in the first frame, 2 atoms in the second frame
and again 2 atoms in the third frame. Is there any workaround for this problem.
I have been thinking for a while but couldn't figure out any solution. Also VMD
also doesn't update the colors in every frame. Can we ask VMD to do this?


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