VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Jan 20 2009 - 10:47:17 CST

Hi,
  Use the "DynamicBonds" representation in combination with the VDW or
other representations, and you should be able to get what you want.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Jan 20, 2009 at 10:40:46AM -0600, nicholas lee wrote:
> Hi,
>
> I want to show bonds breaking when stretched beyond a specified cut-off distance in VMD. What "Drawing Method" should I use? An example of what I would like to see is below.
>
> http://njolee.net/show/eqvide.mpg
>
> Thanks,
>
> Nicholas J. Lee
>
> More details: I am creating movies from LAMMPS trajectory files. I know how to create bond geometries from bond topology files (using source->mol->lmpbondsfromdata,etc), but this is not what I want, because they use fixed topologies. When bond topology is fixed, bonds are drawn between atoms no matter how far they move apart. I do not want this. I want bonds to be drawn only if the distance between atoms is less than a number I specify as shown in the movie above.
>
> 

-- 
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