VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue Jun 28 2011 - 12:56:11 CDT

On Tue, Jun 28, 2011 at 1:23 PM, Debasis Sengupta <dxs_at_cfdrc.com> wrote:
> Hi,
> I have a number if hydrogen molecules in the system.  I am unable to see the
> bond between two atoms in a H2 molecule.  Here is what I tried: Graphics -->
> Representation --> Create Rep --> DynamicBonds. Then set the "type H" and
> set the distance cut-off to 1.0 (H-H bond distance ~0.8A).  The procedure
> works for all other atoms (and atom pairs) except H.  Why isn't working for
> H?  Thanks

because they are explicitly excluded in the bond searching algorithms.

you have to keep in mind that VMD was originally written to handle
data for "bio" systems where bonds between hydrogen atoms don't
happen. if you don't exclude H-H bonds, then the radius based
bond searching heuristics in VMD will produce a lot of spurious H-H bonds.

you can manually add a bond using, e.g. the topotools plugin:
http://sites.google.com/site/akohlmey/software/topotools/topotools---documentation#TOC-addbond-id1-id2-
or (temporarily) rename your atoms to some other name that VMD
won't recognize as hydrogens or non-atom positions.

cheers,
    axel.

> Debasis
> 

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.