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

[Anton Feenstra]

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.

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                                     |
| / \ / \'| | | IBIVU/Bioinformatics - Vrije Universiteit Amsterdam   |
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