VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Wed Nov 14 2007 - 04:07:00 CST

On Tue, 13 Nov 2007, David Schall wrote:

DS> Hello VMD users,

hello david,

DS> I have a set of simulations containing some H2 molecules and a carbon film
DS> which I am trying to visualize using VMD and the dynamic bonds graphic
DS> representation. The dynamic bonds representation draws C-C bonds and C-H
DS> bonds when the bond length is within the cut off distance, but it does not
DS> draw the H-H bonds. Is this a limitation of the dynamic bonds
DS> representation? Can anyone suggest a fix? I'm using a reactive empirical

as far as i remember without having access to the source code,
VMD excludes hydrogen-hydrogen bonds from the regular bond searching.
this is an (empirical) optimization that stems from VMD's origin
in bio systems. as a workaround, can you set the H-H bonds manually?
or do they break and (re-)form. this way you can "cheat" VMD a little
bit, by overloading a static representation with only he H-H bond
with the dynamic bonds for the rest. but in the long run we need a
better dynamics bonds algorithm. the current one fails for almost
anything where the radii of the involved atoms differs a lot or
where you want show bonds where bond-"donor" and bond-"acceptor"
are part of different selections.

cheers,
   axel.

DS> potential so using a distance-based switch like the dynamic bonds rep is
DS> really the only way to go.
DS>
DS> Thanks in advance.
DS>
DS>
DS>
DS> J. David Schall
DS> Assistant Research Professor
DS> Department of Chemistry
DS> United States Naval Academy
DS> 

-- 
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Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   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
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