Erik, Thanks for the explanations! I'm glad to see that the two things that were causing me the main problems aren't bugs.
If the reverse ordering in -hbm and -hbn output isn't a bug, then the documentation certainly needs to be updated. The online and paper manuals say that the -hbm output "Ordering is identical to that in -hbn index file" which obviously is not the case if it is reversed. It would also be nice to include a better description of "Pairs within 0.35 nm" in the documentation. 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] -----Original Message----- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Erik Marklund Sent: Wednesday, August 23, 2006 7:28 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] g_hbond Ok. I'm on it. A few things I can see right away, other things need a closer look. See comments below On Tue, 2006-08-22 at 16:02 -0500, Moore, Jonathan (J) wrote: > 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 > Ok. Thats strange. > - 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. > Well it does make sense, even though it is poorly phrased. See, "Pairs within 0.35 nm" refers to the g(t) function, which in turn is pairs within h-bonding distance, but not fulfilling the angular criterion. Therefore the number of such pairs could very well be less than the number of h-bonds. > - 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 > Will have to look into that, but I'm a bit to occupied to do it right away. > 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. > Nope. I think youre wrong. I believe that the index should be read the other way around. The last row of the index file corresponds to the FIRST row of the hbm-data. Have another look at your ndx:es and hbm:s and you'll find a nice surprise in there. This way of matching the ndx and hbm can be confusing. (I have to admit that I made the same mistake myself not long ago. It cost me and my co- workers a lot of precious time.) I chose not to change it while revising the code though, since I assumed there was some bizarre logic behind it. /Erik > 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 -- 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 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 _______________________________________________ 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
