[gmx-users] g_hbond angle def

[rob yang]

Thank you David, I got it now. For future reference of the list, my initial confusion was because I had misinterpretated that ADH is an alternate *implementation* of DHA. But really, ADH is an independent geometric *definition*.

-Rob

> Date: Fri, 6 Feb 2009 22:32:48 +0100
> From: spoel at xray.bmc.uu.se
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] g_hbond angle def
> 
> rob yang wrote:
> > At the risk of exposing my density in triangle geometry here, why does 
> > 180-DHA = ADH?
> >       H
> >    /     \
> > D ----- A
> 
> This shows it... I confused it even further. The angle we have been 
> using since 3.2 is HDA. If 0, it is perfect, if more than 30 (-acut 
> option) it is not counted anymore.
> 
> Sorry for the confusion.
> > 
> > Thank you.
> > 
> > -Rob
> > 
> >  > Obviously the DHA angle in a linear Hbond is
> >  > 180, so it should either be 180-DHA or ADH. The ADH angle is what's
> >  > implemented in gromacs > 3.2.1, however in 3.1.4 it still was DHA. The
> >  > default maximum angle has changed from 60 in gmx 3.1.4 (based on Kabsch
> >  > and Sander 1983) to 30 (from 3.2.1 onwards, based on other literature).
> >  > So my paper uses ADH, even though it says DHA.
> >  >
> >  > > Thank you.
> >  > >
> >  > > -Rob
> >  > >
> >  > > 
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> -- 
> David van der Spoel, Ph.D., Professor of Biology
> Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
> spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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