From: Axel Kohlmeyer (
Date: Mon Sep 28 2009 - 09:28:03 CDT

On Mon, Sep 28, 2009 at 9:36 AM, Sun Yicheng <> wrote:
> Dear VMD users,
> I need to visualize energy of each atom in each time-step of my
> simulation.
> I have writen a regular PDB file and the numerical values for energy were
> stored in "beta" field,

this will not work. vmd will read "structure" information like atom
and residue names
_and_ the beta field only once and keep that constant. the user field
was added to
overcome this, but right now you have to read the data from an external file and
copy it into the user field step by step.

> then ,
> set sel [atomselect top all]
> $sel set user [$sel get beta]
> does that means all of the value for energy were stored in "user" field?

no. only for the current time step.

> i choose the "user" coloring method in Graphical Representations and "update
> color every frame" in Trajectory,but the color is not changed at each frame.
> I was puzzled by this problem for days,
> any suggestion will be appreciated.

this topic has been discussed on this list many, many time. you
should have spent researching the mailing list archives and you
would have found a number of suggestions.


> Thank you very much.
> 2009-09-28
> ________________________________
> Sun Yicheng
> NanJing University

Dr. Axel Kohlmeyer
Institute for Computational Molecular Science
College of Science and Technology
Temple University, Philadelphia PA, USA.