From: Samuel Jobbins (
Date: Thu Mar 26 2015 - 10:57:51 CDT

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?

Sorry if this is a very mundane question, but I cannot find a solution to this problem!

Thanks for your time,