From: Arham Amouie (
Date: Tue Feb 18 2014 - 05:17:57 CST

I'm grateful for all helpful and informative replies that I received.


On Mon, 2/17/14, John Stone <> wrote:

 Subject: Re: vmd-l: Simplest file format that includes atom color?
 To: "Arham Amouie" <>
 Cc: "Olaf Lenz" <>, "" <>
 Date: Monday, February 17, 2014, 7:17 PM
 The issue here is that most file formats don't actually
 per-timestep data other than
 coordinates or velocities, and the
 plugin interface in VMD was originally written based on
 capabilities (and limitations) of the
 existing file formats used
 in the field. 
 VMD itself can indeed store various types of
 time varying information, but at present this
 is accessible primarily
 through scripting
 interfaces.  We plan to expose this functionality
 through a revised molfile plugin interface
 soon, which will enable
 two or three modern
 trajectory file formats to be able to support this
 type of feature.  All of the
 "legacy" trajectory file formats will still
 have their existing limitations simply because
 they don't have a means of
 anything beyond coordinates, velocities, etc.
 On Sun, Feb 16, 2014 at
 03:44:20AM -0800, Arham Amouie wrote:
 Dear Dr. Olaf Lenz,
> As far as I understand, your nice file
 format assumes that the structure data is time-independent.
 In my case, the quantity which I use for coloring atoms
 changes with time, so I have to save each timestep in a
 seperate file. I don't exactly know how VMD works, but
 It would be more convenient if it was possible to update
 some data in each time step in addition to coordinates.
> Arham
> On Thu, 2/13/14, Olaf Lenz <>
>  Subject:
 Re: vmd-l: Simplest file format that includes atom color?
>  To: "Arham Amouie" <>
>  Cc: ""
>  Date: Thursday, February 13, 2014, 11:48

>  Hi!
>  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
>  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


>  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.
>  Olaf

>  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
 advanceArham Amouei



>  --

>  Dr. rer. nat.
>  Lenz

 Institut für
>  Computerphysik,
 Allmandring 3, D-70569

 StuttgartPhone: +49-711-685-63607

 NIH Center for Macromolecular Modeling and
 Beckman Institute for
 Advanced Science and Technology
 of Illinois, 405 N. Mathews Ave, Urbana, IL 61801      
     Phone: 217-244-3349