[gmx-users] Re: g_hbond

[Jian Zou]

Hi David,

Thank you for the explanation.

Regards,

Jian Zou

----- Original Message ----- 
Date: Fri, 11 Aug 2006 08:24:54 +0200
From: David van der Spoel <spoel at xray.bmc.uu.se>
Subject: Re: [gmx-users] Re: g_hbond
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <44DC22B6.7000602 at xray.bmc.uu.se>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

Jian Zou wrote:
> Hi David,
>
> I read your JPCB paper (JPCB-110-4393) and it says that the geometric
> criteria with DA distance and DHA angle is employed. Therefore I'm a 
> little
> confused which angle is indeed used to determine the Hbond, HDA or DHA?
>
>
Oops, that is wrong in the paper! It is HDA in the program.

In the literature, e.g. the two papers by Starr et al. and the paper by
Xu & Berne it is said that the O-H ... O should be less then thirty
degrees, which is also what I wrote in my paper (DHA) however that does
not make sense, because that angle is more than 90 degrees in a HB.
Sorry about the confusion, but I'm sure that everyone either uses HDA or
HAD. We can reproduce exactly the numbers of Xu & Berne with g_hbond for
TIP4P and SPC/E.