[gmx-users] g_hbond angle def

[David van der Spoel]

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.
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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