Dechang Li wrote: >> ------------------------------ >> >> Message: 4 >> Date: Sun, 18 May 2008 00:50:30 +0200 >> From: "Xavier Periole" <[EMAIL PROTECTED]> >> Subject: Re: [gmx-users] g_hbond distance distribution problem >> To: Discussion list for GROMACS users <gmx-users@gromacs.org> >> Message-ID: <[EMAIL PROTECTED]> >> Content-Type: text/plain;charset=utf-8;format="flowed" >> >>> Dechang Li wrote: >>>> Dear all, >>>> >>>> I used command g_hbond to calculated the distance distribution of >>>> hbonds >>>> in my system. There are two columns in the file hbdist.xvg, as showed >>>> follow: >>>> >>>> @ title "Hydrogen Bond Distribution" >>>> @ xaxis label "Hydrogen - Acceptor Distance (nm)" >>>> @ yaxis label "" >>>> >>>> @TYPE xy >>>> 0.0025 0 >>>> 0.0075 0 >>>> 0.0125 0 >>>> 0.0175 0 >>>> 0.0225 0 >>>> 0.0275 0 >>>> 0.0325 0 >>>> 0.0375 0 >>>> 0.0425 0 >>>> 0.0475 0 >>>> ...... ... >>>> >>>> I think the second column is the distance distribution of hbonds, so >>>> the >>>> summation of the second column should be 1, right? However, the summation >>>> in my file is 200, what is the problem? > >> The sum itself should not be one but the integral of the curve should be >> one. Considering the bin you have the 200 makes sense. Try to integrate. >>> Could be, then it is ot normalized. You can do that easily in xmgrace. > > I integrated it, the result is 1.0 exactly. > >>>> And the first column refered to "Hydrogen - Acceptor Distance (nm)" , >>>> should >>>> it be the distance of donors and acceptor? Am I right? >>> At what position is the top of the distribution? >>> If it is at 0.17 nm it is HA as it says. > > The top of the distribution is about 0.3 nm, so it is the D-A distance? Yes. Will fix it.
> > > >>>> >>>> >>>> >>>> >>>> Best regards, >>>> 2008-5-17 >>>> >>>> >>>> ========================================= >>>> Dechang Li, PhD Candidate >>>> Department of Engineering Mechanics >>>> Tsinghua University >>>> Beijing 100084 >>>> PR China >>>> >>>> Tel: +86-10-62773779(O) >>>> Email: [EMAIL PROTECTED] >>>> ========================================= >>>> >>>> > > > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > 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 -- David van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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
