[gmx-users] cut-off g_hbond

Justin Lemkul jalemkul at vt.edu
Fri Oct 5 13:32:19 CEST 2012

On 10/5/12 7:20 AM, Gavin Melaugh wrote:
> Hi all
> I am using g_hbond to calculate the number of hydrogen bonds in an
> alcohol system. I am using
> the following command:
> g_hbond -f traj.trr -nonitacc
> I am slightly confused about the cut off r. Using the above command, is
> the default cut-off r (0.35nm) for the donor-acceptor distance or the
> hydrogen-acceptor ?

This is controlled by the -da switch.  The default is donor-acceptor; if one 
uses g_hbond -noda, then the cutoff is applied to the hydrogen-acceptor distance.



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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