From: Mihir Tungare (
Date: Mon Mar 29 2010 - 16:34:21 CDT


I am working with a GaN wurtzite structure. I am visualizing the atomic
positions obtained from the LAMMPS trajectory xyz.out file. VMD
automatically chooses certain bonds and I am trying to create the rest of
the bonds for the 3D lattice. There is the Add/Remove Bonds selection under
the Mouse tab that I tried using. However I was able to create bonds
individually and was not able to figure out a way for the software to
automatically create similar bonds across the entire 3D cell. Could someone
let me know my options to be able to do this using VMD?