From: Axel Kohlmeyer (
Date: Thu Mar 26 2015 - 12:08:48 CDT

On Thu, Mar 26, 2015 at 11:57 AM, Samuel Jobbins
<> wrote:
> Hello everyone,
> I have a trajectory of a phase transition in XYZ format, along with
> coordination sphere data for each atom in each frame of the trajectory.
> I am trying to visualise the trajectory on VMD and I would like to colour
> coordinate the atoms by their coordination number. I was planning to do this
> by changing the labels of the atoms in each frame corresponding to their CN,
> such that one could interactively see the evolution of each atom's CN.
> However, I've noticed that VMD seems to only take the labels from the first
> frame of the trajectory, and keep them constant throughout the simulation.
> I have tried using different 'real' atomic labels (such as replacing Zn with
> Cu, Fe, Co etc, depending on CN) as well as dummy labels (eg Zn3, Zn4, Zn5
> to indicate CN). I've also tried using different file types (e.g. pdb).
> However, every time VMD only takes the label from the first frame.
> Does anyone know a way around this?

please check out chapter 5 in this document.

it is a bit dated, but the basic principles are still the same. for
additional details, check the vmd user's guide.

the simplest way to color code using per timestep data is to read a
file and store the data in a user field.


> Sorry if this is a very mundane question, but I cannot find a solution to
> this problem!
> Thanks for your time,
> Sam

Dr. Axel Kohlmeyer
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.