From: Olaf Lenz (
Date: Thu Feb 13 2014 - 02:18:39 CST


As Norman already wrote, it is hard to guess what you really want. I assume
that you want to be able to choose the color of each atom individually.

In VMD, the color of an atom is determined by the "Coloring Method", that
you can choose in the dialog "Graphics -> Representations...". By default,
it uses the "Name" coloring method, which determines the color of the atom
by the first letters of the atom name and colors it accordings to the
element (an atom with the name "C" is a carbon, so it is colored cyan, "H"
is white, ...)

Alternatively, you can color the atoms based on some property of the atom,
e.g. the mass, the charge, beta, and the color scale. To be able to use
that, you will have to set these properties somehow, and this is indeed
something that you should do via the file format.

For cases like yours, I have created the VTF file format, which can be
visualized by VMD:

When you already generate XYZ-files, then transforming them to VTF-files is
simple. In a VTF file, you can modify any of the properties of the atoms.


2014-02-12 20:28 GMT+01:00 Arham Amouie <>:

> Hello
> I've written a MD code for EAM potentials. The typical number of atoms is
> of the order of 1 million. This code saves the positions in xyz files and I
> use VMD for visualization. Now, I'm going to change the output, so that
> each atom can have its particular color. I used csv format of ParaView for
> this reason, but ParaView doesn't work fast for me. What is the easiest
> solution in VMD?
> Thanks in advance
> Arham Amouei

Dr. rer. nat. Olaf Lenz
Institut für Computerphysik, Allmandring 3, D-70569 Stuttgart
Phone: +49-711-685-63607