[gmx-users] g_hbond

[Moore, Jonathan (J)]

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: 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
> 
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-- 
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

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