[gmx-users] g_hbond cut-offs
Alan Wilter Sousa da Silva
alan at biof.ufrj.br
Tue Jan 21 19:15:34 CET 2003
Please, I would like to dismiss any confusion due to the
incongruence between g_hbond help (p. 216) text and GMX Manual 3.1.1 p.
At page 158 H bond is presented as such:
H where cut-offs are:
/ r(D-A) < .35 nm
/ alpha alpha(HD^DA) < 60 degrees
D - - - - A
However, at page 216, we have:
"g_hbond computes and analyzes hydrogen bonds. Hydrogen bonds are
determined based on cutoffs for the angle Donor - Hydrogen - Acceptor
(zero is extended) and the distance Hydrogen - Acceptor."
A which, according to default of 'g_hbond -h' gives:
r / r(H-A) < .25 nm
theta / alpha alpha < 60 deg. -> theta(DH^HA) > 120 deg.
D-------H - - - -
If I interpreted correctly, I believe that the 2nd case is what g_hbond is
surely doing, isn't?
Thanks for any attention.
Alan Wilter S. da Silva
Laboratório de Física Biológica
Instituto de Biofísica Carlos Chagas Filho
Universidade do Brasil/UFRJ
Rio de Janeiro, Brasil
More information about the gromacs.org_gmx-users