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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