[gmx-users] hydrogen bond analysis

[Quyen V. Vu]

> Dear all
> For hydrogen bond analysis, we generate *.xvg file for -num tag in gmx
> hbond command.  My inquiry is in the xvg file there are three column
> output. First column is time. Which one is hydrogen bond number?
> If number 2 column is hydrogen bond number in every frame than what is
> number 3 column.
> """"""
> @    title "Hydrogen Bonds"
> @    xaxis  label "Time (ns)"
> @    yaxis  label "Number"
> @TYPE xy
> @ view 0.15, 0.15, 0.75, 0.85
> @ legend on
> @ legend box on
> @ legend loctype view
> @ legend 0.78, 0.8
> @ legend length 2
> @ s0 legend "Hydrogen bonds"
> @ s1 legend "Pairs within 0.35 nm"
>          0           7          11
>      0.001           8          10
>      0.002           7          11
>      0.003           6          12
>      0.004           7          11
> ?""""""
> Thank you very much in advanced.
> ?
> ?Best Regards.?
>
> --
> *Md Imrul Reza Shishir*
> Master Student
> *Inha University*
>
> As many people explained above, the second column   is number of hydrogen
bond, which satisfy both distance and angle cutoff.
because hydrogen is the interaction between dipole and charge, Interaction
energy has form V=k*p*cos(thetha)/r
p is magnitude of dipole moment, thetha is angle between dipole p and
vector formed by center of dipole and charge.
that is why hydrogen bond concern about both distance and angle
-Quyen