[gmx-users] g_hbond

Moore, Jonathan (J) JMoore2 at dow.com
Tue Aug 22 23:02:48 CEST 2006

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

- 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.

- 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

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


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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