From: Jeffrey Potoff (
Date: Fri Feb 08 2013 - 09:56:22 CST

I suggest the following:
1. Write a script or C/C++ program to convert your XYZ file to PDB format.
2. Pad the PDB file so you always have a constant number of entries.
3. Use the occupancy field to denote whether an entry is real or a filler.
4. For the radius, you could map radius from the XYZ file to an atom
type (which would then be defined in the PDB field). Diameters of atom
types can be defined in VMD, so you can create whatever mapping you need.

Hope this helps,

On 02/08/2013 07:55 AM, Gavin Melaugh wrote:
> Hi All,
> I have been using VMD for the last 3 years to analyse trajectories from
> molecular simulations.
> Recently I have started a new project looking at the population
> dynamics of
> bacterial growth. Since I am used to using VMD I was wondering the
> following:
> 1) Can I load xyz configuration files into VMD, in which the number of
> particles
> (bacterial cells) is different in each configuration file.
> 2) Also if 1) can be achieved, is there also a way of defining the
> radius of
> each individual particle. The output from my simulation gives xyz
> files with the following format
> agent x y z radius
> 1
> 2
> 3
> I can generate movies from the simulations but I just find that I can
> not interact with them in the way that I am used to.
> Many Thanks in Advance
> Gavin

Jeffrey J. Potoff               
Associate Professor                       Wayne State University
Department of Chemical Engineering and Materials Science
5050 Anthony Wayne Dr                     Phone:(313)577-9357		
Detroit, MI 48202                         Fax:  (313)578-5815