[gmx-users] cut-off g_hbond

Gavin Melaugh gmelaugh01 at qub.ac.uk
Fri Oct 5 13:39:13 CEST 2012

Hi Justin

Thanks, that's what I thought. Is there a need to define a
hydrogen-acceptor distance as well. I read in a few articles that this
was the case, usually 0.25nm ?



Justin Lemkul wrote:
> 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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