[gmx-users] Re: g_hbond

Jian Zou zouj01 at mails.tsinghua.edu.cn
Fri Aug 11 12:56:45 CEST 2006

Hi David,

Thank you for the explanation.


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.

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