[gmx-users] Re: Ordering of hydrogen bonds in -hbn and -hbm output in g_hbond

[Justin Lemkul]

On 8/15/12 4:54 PM, Andrew DeYoung wrote:
> Hi again,
>
> I just looked at page 214 in the version 4.5.4 PDF manual (not the -h man
> page), and it says:
>
> "An H-bond existence map can be generated of dimensions # H-bonds X #
> frames. The ordering is identical to the index file (see below), but
> reversed, meaning that the last triplet in the index file corresponds to the
> first row of the existence map."
>
> So this seems to answer my question.  The order is indeed reversed.  I do
> NOT mean this as a criticism, but just politely I would like to say that the
> -h man page for g_hbond may thus be a little vague and potentially
> misleading.
>

We've had these discussions before on the list (several times).  It may be a bit 
confusing at first, but if you think about the numbering of the y-axis in the 
.xpm file, it is numbered like any other, starting with the coordinate origin. 
Thus the values increase upward.  To plot it "backwards" I think would be vastly 
more confusing, and each analysis program (g_hbond, do_dssp, g_mdmat, etc) would 
have to choose whether its output would be written "forward" or "backward" since 
they all share the same code for writing .xpm files.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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