I'm still having problems with g_hbond. I've submitted a bugzilla report.
- The hbond existence matrix in the -hbm output does not match the list of hbonds in the ndx file from -hbn. - Also, it outputs "No option -g" when no -g command line option has been tried - Also, sometimes the number of "Pairs within 0.35 nm" is smaller than the number of "Hydrogen bonds" in the -num output. This makes no sense to me if I understand correctly that "within 0.35 nm" is one of the criteria being used to determine if an hbond exists. - Also, for the groups O5 and 3pos mentioned below, the -hbn .ndx lists the acceptors from both O5 and 3pos groups in [ acceptors_O5 ] and [ acceptors_3ps ] groups, which isn't what I expected I'm using a CVS version, g_hbond.c includes "$Id: gmx_hbond.c,v 1.27 2006/06/15 12:33:03 spoel Exp $" and g_hond -h replies "VERSION 3.3.99_development_20060330" (that sounds to me like it was after the changes made by Erik Marklund...whose email to the developers list is what prompted to go get the CVS code) I ran g_hbond twice for the same xtc file. The first time I choose groups "O5" and "3pos". The second time I choose both groups to be "polymer." O5 and 3pos are both subsets of polymer. 2 hbonds are identified between O5 and 3pos. 16 hbonds are identified between polymer and polymer, including the same 2 identified between O5 and 3pos (as can be seen by finding the same patterns in the existence matrix of the -hbm output). However, the .ndx files from the -hbn output identify the hbonds as being for different sets of donors and acceptors. That is, the triplets 47 48 42 and 19 20 14 are identified from O5/3pos analysis. Those same existence matrix patterns appear in the analysis of polymer/polymer but are identified as 2 1 11 and 64 65 58. 47 48 42 and 19 20 14 are triplets that should be included in a 05/3pos analysis but 2 1 11 and 64 65 58 are not. Thanks, Jonathan ____________________________ Jonathan Moore, Ph.D. Research and Engineering Sciences - New Products Core R&D The Dow Chemical Company 1702 Building, Office 4E Midland, MI 48674 USA Phone: (989) 636-9765 Fax: (989) 636-4019 E Mail: [EMAIL PROTECTED] _______________________________________________ gmx-users mailing list gmx-users@gromacs.org 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