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

Justin Lemkul jalemkul at vt.edu
Wed Aug 15 22:57:59 CEST 2012

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 A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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