From: Axel Kohlmeyer (
Date: Fri Feb 11 2011 - 13:00:56 CST

you can define multiple dynamics bonds representations,
each for groups of atoms.


On Fri, Feb 11, 2011 at 1:01 PM, Debasis Sengupta <> 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

Dr. Axel Kohlmeyer
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.