From: Olaf Lenz (
Date: Mon Feb 17 2014 - 02:44:09 CST


In principle, VMD is not really able to handle the case of time-dependent
properties of the atoms.

However, there is a workaround via Tcl-scripting. Via a Tcl script, you can
modify any properties. If you now do this whenever the timestep changes,
you can basically simulate time-dependent properties. Writing such a script
is a bit tedious, however. You first need to load the time-dependent
properties into Tcl, and then set up a hook that modifies the properties
when the frame is changed.

As you seem to have noted, the VTF plugin provides some support to simplify
the first step: it allows to add "user data" to the timesteps in a VTF file
and can load this data into Tcl via a single command. However, the
corresponding plugin version is not yet in VMD 1.9.1, therefore you will
have to compile it on your own, or you have to get an alpha-version of VMD
1.9.2 (via Biocore).

To compile it, get it from

and adapt the Makefile to your system. To be able to use the user data, you
will have to compile Tcl-support, so you have to install Tcl including the
developments files (tcl.h) on your system.

Once you have done that and loaded the plugin (both the molfile reader
plugin "vtfplugin" and the Tcl-plugin "vtftools"), have a look at the
examples in samples/userdata/


2014-02-16 12:44 GMT+01:00 Arham Amouie <>:

> 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 <> wrote:
> Subject: Re: vmd-l: Simplest file format that includes atom color?
> To: "Arham Amouie" <>
> Cc: "" <>
> Date: Thursday, February 13, 2014, 11:48 AM
> 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 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.
> 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. Olaf
> Lenz
> Institut für
> Computerphysik, Allmandring 3, D-70569
> StuttgartPhone: +49-711-685-63607

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