[gmx-users] g_hbond cut-offs

Alan Wilter Sousa da Silva alan at biof.ufrj.br
Tue Jan 21 19:15:34 CET 2003

Hi List!

	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

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