[gmx-users] cut-off g_hbond

[Justin Lemkul]

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

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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