VMD-L Mailing List

From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Mon Feb 17 2014 - 05:36:01 CST

 

Von: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] Im Auftrag von Olaf Lenz
Gesendet: Montag, 17. Februar 2014 09:44
An: Arham Amouie
Cc: vmd-l_at_ks.uiuc.edu
Betreff: Re: vmd-l: Simplest file format that includes atom color?

 

Hi!

 

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

 

Since when? What about the user defined coloring, with which you can set a value per atom per timestep.

 

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

  https://github.com/olenz/vtfplugin

 

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/

 

Olaf

 

 

2014-02-16 12:44 GMT+01:00 Arham Amouie <erham65t_at_yahoo.com>:

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 <olenz_at_icp.uni-stuttgart.de> wrote:

 Subject: Re: vmd-l: Simplest file format that includes atom color?
 To: "Arham Amouie" <erham65t_at_yahoo.com>
 Cc: "vmd-l_at_ks.uiuc.edu" <vmd-l_at_ks.uiuc.edu>
 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: https://github.com/olenz/vtfplugin/wiki/VTF-format

 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 <erham65t_at_yahoo.com>:

 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 <tel:%2B49-711-685-63607>

  

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