VMD-L Mailing List

From: Debasis Sengupta (dxs_at_cfdrc.com)
Date: Fri Feb 11 2011 - 12:01:44 CST

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