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

Erik Marklund erikm at xray.bmc.uu.se
Wed Apr 24 21:34:25 CEST 2013


Could you please clarify if the hbond existed in frames for which g_sdangle reported a ADH-angle above 30 deg?

Also, bear in mind that the -merge flag is on by default, so another hydrogen may bridge the donor-acceptor gap.


On 24 Apr 2013, at 21:09, kim2811 <kmanibog at iastate.edu> wrote:

> 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.
> -- 
> Kristine
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