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Thank you David, I got it now. For future reference of the list, my initial confusion was because I had misinterpretated that ADH is an alternate *implementation* of DHA. But really, ADH is an independent geometric *definition*.<br><br>-Rob<br><br>> Date: Fri, 6 Feb 2009 22:32:48 +0100<br>> From: spoel@xray.bmc.uu.se<br>> To: gmx-users@gromacs.org<br>> Subject: Re: [gmx-users] g_hbond angle def<br>> <br>> rob yang wrote:<br>> > At the risk of exposing my density in triangle geometry here, why does <br>> > 180-DHA = ADH?<br>> > H<br>> > / \<br>> > D ----- A<br>> <br>> This shows it... I confused it even further. The angle we have been <br>> using since 3.2 is HDA. If 0, it is perfect, if more than 30 (-acut <br>> option) it is not counted anymore.<br>> <br>> Sorry for the confusion.<br>> > <br>> > Thank you.<br>> > <br>> > -Rob<br>> > <br>> > > Obviously the DHA angle in a linear Hbond is<br>> > > 180, so it should either be 180-DHA or ADH. The ADH angle is what's<br>> > > implemented in gromacs > 3.2.1, however in 3.1.4 it still was DHA. The<br>> > > default maximum angle has changed from 60 in gmx 3.1.4 (based on Kabsch<br>> > > and Sander 1983) to 30 (from 3.2.1 onwards, based on other literature).<br>> > > So my paper uses ADH, even though it says DHA.<br>> > ><br>> > > > Thank you.<br>> > > ><br>> > > > -Rob<br>> > > ><br>> > > > <br>> > ------------------------------------------------------------------------<br>> > > > Windows Live Messenger. Multitasking at its finest.<br>> > > > <http://www.microsoft.com/windows/windowslive/messenger.aspx><br>> > > ><br>> > > ><br>> > > > <br>> > ------------------------------------------------------------------------<br>> > > ><br>> > > > _______________________________________________<br>> > > > gmx-users mailing list gmx-users@gromacs.org<br>> > > > http://www.gromacs.org/mailman/listinfo/gmx-users<br>> > > > Please search the archive at http://www.gromacs.org/search before <br>> > posting!<br>> > > > Please don't post (un)subscribe requests to the list. Use the<br>> > > > www interface or send it to gmx-users-request@gromacs.org.<br>> > > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br>> > ><br>> > ><br>> > > --<br>> > > David van der Spoel, Ph.D., Professor of Biology<br>> > > Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.<br>> > > Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.<br>> > > spoel@xray.bmc.uu.se spoel@gromacs.org http://folding.bmc.uu.se<br>> > > _______________________________________________<br>> > > gmx-users mailing list gmx-users@gromacs.org<br>> > > http://www.gromacs.org/mailman/listinfo/gmx-users<br>> > > Please search the archive at http://www.gromacs.org/search before <br>> > posting!<br>> > > Please don't post (un)subscribe requests to the list. Use the<br>> > > www interface or send it to gmx-users-request@gromacs.org.<br>> > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br>> > <br>> > ------------------------------------------------------------------------<br>> > Twice the fun— Share photos while you chat with Windows Live Messenger. <br>> > <http://www.microsoft.com/windows/windowslive/messenger.aspx><br>> > <br>> > <br>> > ------------------------------------------------------------------------<br>> > <br>> > _______________________________________________<br>> > gmx-users mailing list gmx-users@gromacs.org<br>> > http://www.gromacs.org/mailman/listinfo/gmx-users<br>> > Please search the archive at http://www.gromacs.org/search before posting!<br>> > Please don't post (un)subscribe requests to the list. Use the <br>> > www interface or send it to gmx-users-request@gromacs.org.<br>> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br>> <br>> <br>> -- <br>> David van der Spoel, Ph.D., Professor of Biology<br>> Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.<br>> Box 596, 75124 Uppsala, Sweden. Phone:        +46184714205. Fax: +4618511755.<br>> spoel@xray.bmc.uu.se        spoel@gromacs.org http://folding.bmc.uu.se<br>> _______________________________________________<br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://www.gromacs.org/mailman/listinfo/gmx-users<br>> Please search the archive at http://www.gromacs.org/search before posting!<br>> Please don't post (un)subscribe requests to the list. Use the <br>> www interface or send it to gmx-users-request@gromacs.org.<br>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br><br /><hr />Twice the fun— <a href='http://www.microsoft.com/windows/windowslive/messenger.aspx' target='_new'>Share photos while you chat with Windows Live Messenger.</a></body>
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