On Wed, 2006-08-02 at 15:59 +0200, Erik Marklund wrote: > On Wed, 2006-08-02 at 13:50 +0100, Una Bjarnadottir wrote: > > Dear users, > > > > I want to use the -sel option in g_hbond and selected three hydrogen > > bonds to analyse. I choose the atom number according to the .gro file > > used to make the index file which had the > > [ selected atoms] > > 20 21 24 > > 25 26 29 > > 34 35 37 > > as it says in the manual: Donor Hydrogen Acceptor: When running the > > g_hbond with the -sel option and chose my group it always comes > > segmentation fault but it ran when I didn't use the -sel option and > > calculated the number of hydrogen bonds as a function of time. > > Is this a bug or is it something wrong with how I made the .ndx file? > > > > I think that in recent versions of g_hbond the -sel option does not work > at all. I don't know if it ever worked. It is a known bug. You will have > to find another way of doing your analysis or fix the bug yourself, the > latter being far from trivial I think. >
Furthermore, if you use the -ac, -life or -hbm options I recommend using the latest version of g_hbond from the cvs repository, since it contains some bug fixes affecting the reliability of -ac, -life and -hbm output. It also provides an index file matching the hbm.xpm file when -merge is used, which wasn't the case in previous versions. /Erik > /Erik > > > Best regards, Una Bjarnadottir > > _______________________________________________ > > 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 -- Erik Marklund, PhD Student, Molecular Biopcysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: +46 18 471 4537 fax: +46 18 511 755 [EMAIL PROTECTED] _______________________________________________ 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
