[gmx-users] any other criteria for h-bond?

kim2811 kmanibog at iastate.edu
Wed Apr 24 21:09:16 CEST 2013

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 g_sgangle to
measure the angle A-D-H of two hydrogen bonds identified when I determined
the hydrogen bonds using g_hbond. What I did is, I separated A-D and H-D as
two groups (i made the atom indices in the order A-D and H-D in the index
file) and measured the angle between these two vectors. However, 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.


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