From: Axel Kohlmeyer (
Date: Fri Apr 01 2011 - 11:59:54 CDT

On Fri, Apr 1, 2011 at 12:07 PM, Saketh Bharadwaja <> wrote:
> Hi,
> Please find attached my VMD input file spit out by LAMMPS. I have a total of
> 801 atoms with the first 400 fixed and the rest 401 moving. I want bonds to
> be created among the atoms to understand the lattice structure better and
> run the movie. Could somebody please tell me how bonds are created
> automatically. I tried creating bonds manually selecting the bonds under
> mouse tab in the VMD console but I want them to be done automatically.

it won't work fully automatically, but explanations and some suggestions
on how to make it work are given here:


> Regards,
> Saketh.

Dr. Axel Kohlmeyer
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.