From: Kristine Manibog (
Date: Tue Apr 23 2013 - 19:39:17 CDT

Hi, is there any other criteria in determining a hydrogen bond? i know that
in order for a bond to exist, donor-acceptor distance should be less than
or equal 3.5A and A-D-H angle less than or equal 30deg. I used VMD to
visualize two hydrogen bonds using cut-offs mentioned above and it showed
that these two hydrogen bonds exist. However, when I try to measure the D-A
distance and A-D-H angle separately through entire simulation time, the
A-D-H angle as a function of time fall above the cut-off of 30deg and I
wonder why. is there any other explanation for this?

thank you.