From: Justin Gullingsrud (
Date: Sun Aug 21 2005 - 15:55:04 CDT


Here's a script that might get you started. It processes your
trajectory and stores the distance moved by each atom in the 'user'
field. To view the results, set the coloring method of one of your
reps to "User", then go into the Trajectory tab in the Graphics menu
and check the "Update Color Every Frame" box. If the "Color Scale
Data Range" shows "0" and "0", try changing to the last timestep in
your trajectory (using the animation controls), then hit the Autoscale
button in the Trajectory tab to rescale the colors. You can also set
the scale range manually. If you want the colors to be something a
little more sensible, like red-white-blue for small-medium-big, bring
up the Colors menu (it's under the Graphics pulldown menu in the Main
palette), choose the Color Scale tab, and select RWB in the Method


On 8/18/05, Jaime Sanchez <> wrote:
> Dear VMD users,
> I'm using LAMMPS to represent surface melting. I wanted to know if there's a
> way that I can change the color of the atoms that have larger velocities in
> relation to the rest of the lattice. It's hard to visualize which atoms are
> moving when the number of atoms is too large.
> Thanks
> Jaime Sanchez

The spirit of Plato dies hard.  We have been unable to escape the
philosophical tradition that what we can see and measure in the world
is merely the superficial and imperfect representation of an
underlying reality.
                -- S.J. Gould, "The Mismeasure of Man"