[gmx-users] distance and angle cutoff for hydrogen bond

atila petrosian atila.petrosian at gmail.com
Sat Jul 30 14:10:42 CEST 2011

Dear gromacs users

in gromacs manual, there is [-a real 30 Cutoff angle (degrees, Acceptor -
Donor - Hydrogen)
-r real 0.35 Cutoff radius (nm, X - Acceptor, see next option)]

I think that in hb (D-H...A) distance of 0.35 nm = distance between D and A.

and angle of 30 = acceptor-donor–hydrogen angle.

is my think true?

if I want following criterion for hydrogen bond analysis, is [ -r 3.5 and -a
135 ] true?

donor-acceptor distance (dDA) ≤ 3.5 Å  and the donor–hydrogen-acceptor angle
(αDHA) ≥ 135°.

any help will highly appreciated.
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