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

Andrew DeYoung adeyoung at andrew.cmu.edu
Wed Aug 15 22:54:00 CEST 2012

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


Andrew DeYoung
Carnegie Mellon University

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