VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
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.

cheers,
   axel.

YS>
YS> Thanks for time
YS> Stanley
YS>
YS>
YS> 

-- 
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Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
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