From: Norman Geist (
Date: Mon Feb 17 2014 - 06:08:07 CST



You can access this values via atomselect. Example:


set a [atomselect top “index 1”]

$a frame 0

$a set user $myvalue


So by using loops and maybe read you values from a simple text file you set individual values for all atoms, like you want. If you need help for the script, describe how your values look like.


Norman Geist.


Von: [] Im Auftrag von Olaf Lenz
Gesendet: Montag, 17. Februar 2014 12:49
An: Norman Geist
Cc: VMD Mailing List
Betreff: Re: vmd-l: Simplest file format that includes atom color?




2014-02-17 12:36 GMT+01:00 Norman Geist <>:

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.



Do you refer to the "Trajectory->User" coloring methods? I would be very interested to learn how this works or is intended to work. There does not seem to be any documentation on that anywhere, or is there?




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