VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Sun Apr 11 2010 - 23:07:21 CDT

Hi,
  You can use the atomselect "getbonds" or "setbonds" subcommands
to manipulate bonds by script, or you may wish to use a tool like
Axel Kohlmeyer's topotools plugin, which is likely much easier to use:
  http://www.ks.uiuc.edu/Research/vmd/plugins/topotools/

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Mar 29, 2010 at 05:34:21PM -0400, Mihir Tungare wrote:
> Hi,
>
> 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?
>
> Thanks,
> Mihir. 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078