[gmx-users] g_hbond

Erik Marklund erikm at xray.bmc.uu.se
Wed Aug 23 13:27:52 CEST 2006

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

> 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.


> 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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