From: Arham Amouie (
Date: Tue Feb 18 2014 - 04:52:20 CST

I use VMD 1.9.1 but upgraded "vtfplugin" to last version. Reading from compressed files is a good idea. I'll try. Thanks.


On Tue, 2/18/14, Olaf Lenz <> wrote:

 Subject: Re: vmd-l: Simplest file format that includes atom color?
 To: "Arham Amouie" <>
 Cc: "" <>
 Date: Tuesday, February 18, 2014, 1:51 PM
 comment: the ability to have multiple atom lines for a
 single atom is broken in the plugin of VMD 1.9.1, so you
 have to use the current version, or VMD 1.9.
 However, to reduce the file size it is much simpler to
 compress the files: When the plugin is compiled with zlib
 support (_USE_ZLIB) you can simply gzip the files and the
 plugin can read the files still. To be able to do that, you
 have to install the zlib (including devel files).
 2014-02-18 10:59 GMT+01:00
 Arham Amouie <>:
 Thank you
 for good explanations.  Another feature of the new version
 of "vtfplugin" that is nice is the ability to have
 multiple atom lines for each atom. For systems containing
 many atoms that the number of atom types is small, this
 helps to reduce file size. Another possible way to reduce
 file size is to write coordinates in binary format.
 Now my code can write in VTF format, and I tested it for an
 alloy-system of 2 million atoms.
 Thanks again
 On Mon, 2/17/14, Olaf Lenz <>
  Subject: Re: vmd-l: Simplest file format that includes
 atom color?
  To: "Arham Amouie" <>
  Cc: ""
  Date: Monday, February 17, 2014, 12:14 PM
  In principle,
  VMD is not really able to handle the case of
  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,
  You first need to load the time-dependent properties
  Tcl, and then set up a hook that modifies the
  when the frame is changed.
  As you seem to have noted, the
  VTF plugin provides some support to simplify the first
  it allows to add "user data" to the timesteps in
  VTF file and can load this data into Tcl via a single
  command. However, the corresponding plugin version is
  yet in VMD 1.9.1, therefore you will have to compile it
  your own, or you have to get an alpha-version of VMD
  (via Biocore).
  To compile it, get it
  adapt the Makefile to your system. To be able to use
  user data, you will have to compile Tcl-support, so you
  to install Tcl including the developments files (tcl.h)
  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
  2014-02-16 12:44 GMT+01:00
  Arham Amouie <>:
  Dear Dr.
  Olaf Lenz,
  As far as I understand, your nice file format assumes
  the structure data is time-independent. In my case, the
  quantity which I use for coloring atoms changes with
  so I have to save each timestep in a seperate file. I
  don't exactly know how VMD works, but It would be
  convenient if it was possible to update some data in
  time step in addition to coordinates.
  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 AM
   Norman already wrote, it is hard to guess what you
   want. I assume that you want to be able to choose the
   of each atom individually.
   In VMD, the color of an atom is
   determined by the "Coloring Method", that
   choose in the dialog "Graphics ->
   Representations...". By default, it uses the
   "Name" coloring method, which determines
   of the atom by the first letters of the atom name and
   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,
   mass, the charge, beta, and the color scale. To be
   use that, you will have to set these properties
   this is indeed something that you should do via the
   For cases like yours, I
   have created the VTF file format, which can be
   When you already generate
   XYZ-files, then transforming them to VTF-files is
   a VTF file, you can modify any of the properties of
   2014-02-12 20:28 GMT+01:00
   Arham Amouie <>:
    written a MD code for EAM potentials. The typical
   atoms is of
    the order of 1 million. This code saves the
   xyz files and I
    use VMD for visualization. Now, I'm going to
   output, so that
    each atom can have its particular color. I used csv
   of ParaView
   for this reason, but ParaView doesn't work fast
   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
  Dr. rer. nat. Olaf Lenz
  Institut für Computerphysik,
  Allmandring 3, D-70569 StuttgartPhone:
 Dr. rer. nat. Olaf Lenz
 Institut für Computerphysik,
 Allmandring 3, D-70569 StuttgartPhone: