On Wed, 2006-08-23 at 07:38 -0500, Moore, Jonathan (J) wrote: > 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.
Yes. This surely deserved some better documentation. As I said, the reason for this reversed order is unknown to me and has eluded me once. One of my co-workers, much more perceptive than me apparently, brought it my attention after several weeks of work on some h-bond stuff. > > It would also be nice to include a better description of "Pairs within 0.35 > nm" in the documentation. > Yes, I agree. I changed some of the legends in the latest two cvs versions I think, but let the "Pairs within 0.35 nm" stay the way it was since the legends should be kept fairly short in my opinion. "Pairs within 0.35 nm, but with angle > 30o" might be a bit too long. h(t) and g(t) might be better choices, but it requires some knowledge about the h-bond terminology that gromacs has adopted. > 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
