From: Uday K. Chippada (
Date: Tue Sep 14 2004 - 16:38:20 CDT


I have a simple question on VMD. I am working on a protein and did SMD simulations on it in NAMD. After the simulation I am visualizing it in VMD, and I want to calculate the total number of hydrogen bonds (for a particular distance cut off say 3.0 and a particular angle cut off of say 30) at each frame. I want to know if there is a method to display the number of hydrogen bonds or at least count them.

Any help would be greatly appreciated.

Thank you.
Uday Chippada.