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?
Could be, then it is ot normalized. You can do that easily in xmgrace. > > 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. > > > > > > 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 [email protected] > 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 [email protected] 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
