[gmx-users] g_hbond routine

Velia Minicozzi velia.minicozzi at roma2.infn.it
Fri Nov 30 16:41:58 CET 2012

Dear gromacs users,

in the Gromacs manual pages (version 4.5.3 page 211) there are the 
criteria to have an Hbond.
r < 0.35 nm, where r is the Donor-Acceptor distance
alpha < 30°, where alpha is the Hydrogen-Donor-Acceptor angle

in the Manual page for g_hbond (version 4.5.3 page 275) it is written
"Hydrogen bonds are determined based on cutoffs for the
angle Acceptor - Donor - Hydrogen (zero is extended) and the distance 
Hydrogen - Acceptor"

and even in the file that exits by using the option -dist the xaxis 
label is "Hydrogen - Acceptor Distance (nm)"
but I think this is the Donor-Acceptor distance because it seems too big 
to be the Hydrogen-Acceptor distance.
Which distance is it?

Thank you very much,


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