From: Arham Amouie (
Date: Thu Feb 13 2014 - 05:06:07 CST

Thanks. I knew about coloring by element. I'm searching for a file-format that contains some physical quantity of atoms, like speed, and allows coloring based on that quantity. And I need it to be simple enough, because I don't have enough time to work a lot on input/output of my code. I guess your file format may be what I'm looking for. I'll take a serious look at it. Sorry if my english is bad!


On Thu, 2/13/14, Olaf Lenz <> wrote:

 Subject: Re: vmd-l: Simplest file format that includes atom color?
 To: "Arham Amouie" <>
 Cc: "" <>
 Date: Thursday, February 13, 2014, 11:48 AM
 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
 For cases like yours, I
 have created the VTF file format, which can be visualized by
 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
 2014-02-12 20:28 GMT+01:00
 Arham Amouie <>:
  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 advanceArham Amouei
 Dr. rer. nat. Olaf
 Institut für
 Computerphysik, Allmandring 3, D-70569
 StuttgartPhone: +49-711-685-63607