From: Axel Kohlmeyer (
Date: Sat Oct 30 2010 - 10:56:04 CDT

On Sat, Oct 30, 2010 at 12:47 AM, Wang Xianqiao <> wrote:
> Dear all VMDs,
> I try to plot contour figures of atoms. Contour figures may be trajectories,
> or other field quantities of atoms (I can get outside the input file).

i don't understand what you are asking for.
can you give some example of how this should
look like and how this would be computed?

> Or if there is a way to allow one to use different name to represent the
> same atom in different frame in XYZ format. For example, I have 10 atoms
> first frame have the same name C, but in the second frame, I want to change
> the first five as D according to some quantities. But I can not show
> different color in the second frame. Many thanks,

yes. this is not a bug, this is a feature. it has been discussed on this
list _many_ times before. make sure you check the archives. VMD has
been optimized for classical bio simulations and there atom identities
don't change. you have to keep in mind, that the .xyz file format is about
the worst possible format, since it is the lowest common denominator.

you can store time varying per atom properties in the user, user2, user3,
user4 fields and then use that to color or select atoms. there are other,
more elaborate schemes possible, by tracing the frame counter for your
molecules. those require some knowledge of Tcl (or Python). some Tcl
examples are presented in this pdf


> Best,
> Xianqiao Wang

Dr. Axel Kohlmeyer
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.