[gmx-users] H-D-A angle in H-bond

[Justin Lemkul]

On 3/4/13 7:54 AM, mcapar wrote:
> Dear GROMACS users,
>
> In gromacs, the default values of the geometrical criterion of H-bond are
> 0.35 nm and 30 deg for spc water molecules. The acceptor and donor atoms of
> H-bond in my system are different than in the water system. Therefore I
> think that I should use suitable D-A distance and H-D-A (alpha) angle for my
> system in order to  calculate the number of H-bond. I obtained the D-A
> distance and the A-H-D angle from Cambridge Structural Database (CSD) but I
> couldn’t find the H-D-A  angle from CSD.
>
> I want to learn how I can obtain the H-D-A (alpha) angle.  If you can answer
> me, I’ll be so glad.
>

The default settings do not apply just to SPC; in fact, they come from average 
values obtained from crystallographic databases.  There are a few threads with 
fairly extensive discussions on this topic.  Most papers that I see use similar, 
if not identical, settings to g_hbond.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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