VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Fri Jun 14 2013 - 00:21:33 CDT

On Fri, Jun 14, 2013 at 6:01 AM, Solen <solen_at_brandeis.edu> wrote:
> Hi
>
> I want to visualize atomic structures in a way that I can show how radii of
> the different particles vary. My coordinate file has a fourth dimension for
> the radius of the particles. Is this possible with VMD? and how?

not without some scripting. since radius is not a per timestep
property. please have a look at this document. in section 5.4 there is
an example for changing the charge of particles (another global-only
property) dynamically in a trajectory. you could adapt this for
modifying the radius instead.

https://sites.google.com/site/akohlmey/redirect/cpmd-vmd.pdf?attredirects=0&d=1

this has been used for visualizing results from eFF simulations with
LAMMPS in the past.
http://lammps.sandia.gov/movies.html#eff

axel.

>
> Thank you so much
> Solen
> 

--
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
International Centre for Theoretical Physics, Trieste. Italy.