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 <[EMAIL PROTECTED]> Subject: Re: [gmx-users] Re: g_hbond To: Discussion list for GROMACS users <[email protected]> Message-ID: <[EMAIL PROTECTED]> 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. _______________________________________________ gmx-users mailing list [email protected] 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
