[gmx-users] RE: Bonds and atom-pairs in g_hbond
Justin A. Lemkul
jalemkul at vt.edu
Mon Jun 11 23:49:45 CEST 2012
On 6/11/12 5:41 PM, Andrew DeYoung wrote:
> Hi again,
> I just realized that the output from g_hbond using the -num flag (by
> default, the file name is hbnum.xvg) also seems to make a distinction
> between "hydrogen bonds" and "pairs within the distance." For example, here
> are the first few lines of this output file:
> @ s0 legend "Hydrogen bonds"
> @ s1 legend "Pairs within 0.227905 nm"
> 0 39 1
> 0.05 40 2
> 0.1 40 2
> 0.15 40 1
> 0.2 41 0
> 0.25 38 3
> 0.3 39 2
> where 0.227905 nm is the value that I give to -r. Why are there so many
> more "hydrogen bonds" than "pairs within -r", if the latter seems to be a
> necessary but not sufficient condition for the former?
They are separate quantities. Either an atom pair is a hydrogen bond, or it is
not. You have lots of hydrogen bonds (satisfying both distance and angle
criteria), and a few atom pairs that satisfy distance only. By playing with the
value passed to -a you can change how many are in each column (just an exercise,
not necessarily useful).
Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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