>------------------------------ > >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? >>> >>> >>> >>> >>> >>> 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