From: Axel Kohlmeyer (
Date: Tue Mar 18 2008 - 22:25:27 CDT

On Tue, 18 Mar 2008, Stanley, Yemin Shi wrote:

YS> Dear all,

dear stanley,

YS> I have a question on the displaying setting of a bond breaking
YS> procedure. Basically, I have an .xmol trajectory file. The reaction
YS> site involves an S-H and an N. The S--H bond is suppose to break up
YS> (2.18A) and H--N bond formated (1.2A) through the trajectory. This
YS> is properly displayed in Molden. When it comes to VMD, neither the
YS> S--H break nor the H--N bond form? Any suggestions pls.

use a dynamic bonds representation.

VMD was initially written for classical MD and
there you don't have to recompute the bonding info
(which makes it _much_ faster for large systems).

this topic has been discussed a lot on the mailing
list, so please also search through the list archives.


YS> Thanks for time
YS> Stanley

Axel Kohlmeyer
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
If you make something idiot-proof, the universe creates a better idiot.