[gmx-users] g_hbond

[Erik Marklund]

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