VMD-L Mailing List

From: Harindar Keer (hkeer_at_uci.edu)
Date: Thu Dec 18 2008 - 17:59:34 CST

Dear all,

 I am somewhat confused by the known issue listed in the VMD guide
(Known Issue: The output of hbonds cannot be considered 100% accurate if
the donor and acceptor selection share a common set of atoms)

I am evaluating the number of h-bonds in a selection of water molecules
itself. I am using following command

measure hbonds $cutoff $angle $selection

I would like to confirm whether the list of h-bonds obtained is 100%
accurate. I would sincerely appreciate if some one can clarify this
issue for me. Many thanks.

Warm regards,
Harindar Keer