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

[Erik Marklund]

----- Original Message ----- 
From: "Anton Feenstra" <feenstra at few.vu.nl>
To: "Discussion list for GROMACS development" <gmx-developers at gromacs.org>
Sent: Thursday, August 24, 2006 9:15 AM
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?
>
> There is a reason for this. If you convert the xpm to an image (i.e., 
> using xpm2ps, or even 'convert hbm.xmp hbm.gif'), I would be inclined to 
> read the graph from the bottom up. This means the first Hbond is at the 
> bottom in the figure, but this is the last one in the xpm file. This then 
> corresponds to the first hbond in the .ndx file.
>

Aah. I knew I had heard an explenation at some point, but couldn't remember 
what it was. In a way it all makes sense. Still, I'll be sticking to the 
existing code and will just change the docs.

/Erik

> Feel free to disagree and change things accordingly. This is just my view 
> (I put this in the program in the first place), and may not be the view of 
> the common g_hbond user... ;-)
>
> -- 
> Groetjes,
>
> Anton
>
>  _____________ _______________________________________________________
> |             |                                                       |
> |  _   _  ___,| K. Anton Feenstra                                     |
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