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
--
========================================
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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