[gmx-users] RE: Bonds and atom-pairs in g_hbond

[Justin A. Lemkul]

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

-- 
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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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