[gmx-users] g_hbond routine

Justin Lemkul jalemkul at vt.edu
Fri Nov 30 16:50:32 CET 2012

On 11/30/12 10:41 AM, Velia Minicozzi wrote:
> 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?

It depends on what you select.  You control whether it is the H-A or D-A 
distance using the -da flag.  By default, it is a D-A distance.  There is small 
output bug was reported this morning and there is an open Redmine issue for it. 
  It is low-priority, but will be fixed sometime in the future.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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