From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Apr 15 2011 - 16:24:55 CDT

Debasis,
  There's not currently a way to restrict the dynamic bonds representation
to operate only on a particular pair of atom types, so I'm afraid there's
not much you can do in this specific case. I've been looking into adding
support for secondary atom selections to help with cases like this one,
and for use with the "Polyhedra" representation where one wants to restrict
the representations to specific pairs of atom types. If things go well, I
may get this implemented in a new version of VMD later this year, but I can't
promise it yet.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Apr 14, 2011 at 01:07:56PM -0400, Debasis Sengupta wrote:
> Alex,
> Thanks. I tried creating multiple representation of dynamics bond. For
> example, to draw C and O bond, I set "type C O" and distance cut-off as
> 1.7A. However, it seems like it connects C-C and O-O which are below
> 1.7A, in addition to C-O that are below 1.7A. I just want to connect
> C-O that are below 1.7A.
> Thanks
> Debasis
> On 2/11/2011 2:00 PM, Axel Kohlmeyer wrote:
> >you can define multiple dynamics bonds representations,
> >each for groups of atoms.
> >
> >cheers,
> > axel.
> >
> >On Fri, Feb 11, 2011 at 1:01 PM, Debasis Sengupta<dxs_at_cfdrc.com> wrote:
> >>Hi,
> >>I am looking for an option to set up different bond lengths for different
> >>atom pairs. I am trying visualize a reactive MD trajectory and I used
> >>"DynamicBonds" where there is an option (Distance Cutoff) to set a bond
> >>length which seems to be a global setting. By setting it to a higher
> >>value,
> >>say, 2.1A, connects anything that is up to 2.1A. How can I make, say, O-H
> >>as
> >>1.2A, Si-O as 2.1A, and Si-H as 1.6, so that only O-H up to 1.2A, Si-O
> >>up
> >>to 2.1A and Si-H up to 2.6A are connected in all frame of the trajectory?
> >>Setting a "Distance Cutoff" to 2.1A make O-H connected when they are
> >>larger
> >>than 1.2A.
> >>Thanks
> >>Debasis
> >>
> >>
> >
> >

-- 
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