From: John Stone (
Date: Mon Feb 17 2014 - 09:47:17 CST

  The issue here is that most file formats don't actually allow
per-timestep data other than coordinates or velocities, and the
molfile plugin interface in VMD was originally written based on the
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
storing 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 <> 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

NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
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