Moore, Jonathan (J)
JMoore2 at dow.com
Wed Aug 23 14:38:02 CEST 2006
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.
Jonathan Moore, Ph.D.
Research and Engineering Sciences - New Products
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
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
> - 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
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.
> 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
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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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