VMD-L Mailing List

From: nicholas lee (nicholjl_at_usc.edu)
Date: Tue Jan 20 2009 - 10:40:46 CST

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.