[gmx-users] g_hbond cut-offs

[David]

On Tue, 2003-01-21 at 19:15, Alan Wilter Sousa da Silva wrote:
> 
> Hi List!
> 
> 	Please, I would like to dismiss any confusion due to the
> incongruence between g_hbond help (p. 216) text and GMX Manual 3.1.1 p.
> 158.
> 
> 	At page 158 H bond is presented as such:
> 
>            H          where cut-offs are:
>           /           r(D-A) < .35 nm
>          / alpha      alpha(HD^DA) < 60 degrees
> 	D - - - - A
>              r
> 
> 	However, at page 216, we have:
> 
> "g_hbond computes and analyzes hydrogen bonds. Hydrogen bonds are
> determined based on cutoffs for the angle Donor - Hydrogen - Acceptor
> (zero is extended) and the distance Hydrogen - Acceptor."
> 
>                    A   which, according to default of 'g_hbond -h' gives:
>                   /
>                r /          r(H-A) < .25 nm
>          theta  / alpha     alpha < 60 deg.  -> theta(DH^HA) > 120 deg.
>        D-------H - - - -
> 
> If I interpreted correctly, I believe that the 2nd case is what g_hbond is
> surely doing, isn't?
Yes. It computes them correctly. If the manual is inconsistent, sorry
about that.
> 
> Thanks for any attention.
> 
> Cheers,
> 
> -----------------------
> Alan Wilter S. da Silva
> -----------------------
>  Laboratório de Física Biológica
>   Instituto de Biofísica Carlos Chagas Filho
>    Universidade do Brasil/UFRJ
>     Rio de Janeiro, Brasil
> 
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell and Molecular Biology
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++