VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Sat Jul 20 2013 - 06:42:50 CDT

On Sat, Jul 20, 2013 at 12:36 PM, amit kunte <amit7kunte_at_gmail.com> wrote:
> Hi vmd users
> I have a lammps dump file where the number of atoms change per
> timestep(due to fix pour). I want to visualize it in vmd and I know the
> subsequent limitation of vmd of variant atom visualization and that
> readvarxyz circumvents this problem. Is there a way to visualize with native
> lammps file without converting it to XYZ format? ( If i am not wrong, XYZ

you would have to write a parser similar to the xyz format parser for topotools.

> does not contain diameter info of particles and i have a polydisperse

if you assign a different atom type for each radius, you can handle
this with .xyz format as well. all you'd need is to run a little Tcl
script in VMD after loading the .xyz file that assigns the
corresponding radii to the atom types.

> system to visualize). If no other way please suggest me a tool to convert
> lammps dump to xyz file.

i don't know. have you checked out Pizza.py?

axel.

> Regards
> Amit 

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