[gmx-developers] [Fwd: RE: [gmx-users] g_hbond]

Moore, Jonathan (J) JMoore2 at dow.com
Wed Aug 23 16:44:06 CEST 2006

To me, replacing the legends with h(t) and g(t) (though more informative for the GROMACS expert) is even less helpful to the average user because it is more obscure.  The better option to me is to add an explanation to the online, paper, and -h documentation.  Right now, the explanation for -num simply says "number of hydrogen bonds as a function of time", i.e. doesn't mention the pairs within 0.35 at all.  You could simply add to the documentation the explanation that you gave me "Pairs within 0.35 nm, but with angle > 30o.

About the ordering of -hbn and -hbm output, the main point is to clearly define in the documentation what the orders are.  I typically post-process my output with perl scripts, so it's a little more complicated that I have to go in reverse order to match hbond existence with hbond identity...but now that I know it, now I can do 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

-----Original Message-----
From: gmx-developers-bounces at gromacs.org [mailto:gmx-developers-bounces at gromacs.org] On Behalf Of David van der Spoel
Sent: Wednesday, August 23, 2006 10:04 AM
To: Discussion list for GROMACS development
Subject: Re: [gmx-developers] [Fwd: RE: [gmx-users] g_hbond]

Erik Marklund wrote:
> So how about it? There are still some oddities in g_hbond, especially 
> the order of the entries in hbn.ndx and hbm.xpm. Could anybody explain 
> why the ordering is the way it is? Wouldn't it be wiser to reverse the 
> order one of the files? It sure seems more intuitive to me. If not, 
> someone ought to change the documentation to avoid confusion. That 
> someone could be me of course. What do you people think?
> How about changing the "Hydrogen bonds..." and "Pairs..." legends? 
> (see
> below) Would h(t) and g(t) be a better choice? This is not a big issue,
> but it might as well be dealt with while we're at it.

No problem. I don't think there are lots of scripts (unless your own) 
that depend on the order of things. Clearer is alwyas better, in 
particular since one can turn off xvgr specific output with the -noxvgr 

> /Erik
> -------- Forwarded Message --------
>>From: Erik Marklund <erikm at xray.bmc.uu.se>
>>Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>>To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>>Subject: RE: [gmx-users] g_hbond
>>Date: Wed, 23 Aug 2006 14:50:16 +0200
>>On Wed, 2006-08-23 at 07:38 -0500, Moore, Jonathan (J) wrote:
>>>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.
>>Yes. This surely deserved some better documentation. As I said, the 
>>reason for this reversed order is unknown to me and has eluded me 
>>once. One of my co-workers, much more perceptive than me apparently, 
>>brought it my attention after several weeks of work on some h-bond 
>>>It would also be nice to include a better description of "Pairs 
>>>within 0.35 nm" in the documentation.
>>Yes, I agree. I changed some of the legends in the latest two cvs 
>>versions I think, but let the "Pairs within 0.35 nm" stay the way it 
>>was since the legends should be kept fairly short in my opinion. 
>>"Pairs within 0.35 nm, but with angle > 30o" might be a bit too long. 
>>h(t) and
>>g(t) might be better choices, but it requires some knowledge about the
>>h-bond terminology that gromacs has adopted.
>>>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
>>>>- 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 
>>>>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 
>>>>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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David. ________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
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spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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