VMD-L Mailing List

From: Aditya Padhi (adi.uoh_at_gmail.com)
Date: Tue Nov 01 2011 - 03:53:57 CDT

Dear VMD users,
                We know that from VMD we can get all the possible hydrogen
bonds as well as its associated percentage occupancy from a MD trajectory
file. But I want to get the distance among the donor and acceptor for all
the H-bonds obtained from the MD trajectories. I know that the default
distance is 3 Angstrom and angle of 20 degrees.
                 If any one can help in getting the distances for every
donor-acceptor atoms throughout the simulation I would be grateful. If any
coding is required for this purpose, kindly let me know.

Thanks and regards
Aditya.