[gmx-users] g_hbond

Wed Aug 23 14:50:16 CEST 2006

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: jmoore2 at dow.com
> 
> 
> -----Original Message-----
> From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org]
> 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: jmoore2 at dow.com
> > 
> > _______________________________________________
> > gmx-users mailing list    gmx-users at 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 gmx-users-request at gromacs.org.
> > 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
erikm at xray.bmc.uu.se