[gmx-users] Calculating h-bonds frequency along the simulation

Erik Marklund erik.marklund at chem.ox.ac.uk
Wed Jan 7 22:49:10 CET 2015

> On 7 Jan 2015, at 16:08, Vered Kunik <vered at ofranlab.org> wrote:
> Dear gromacs users,
> I am rather new to gromacs and would very much appreciate your help. I have
> several MD runs of an ATP binding protein (WT versus several mutants). I
> would like to calculate the frequency of H-bonds between the protein and
> the ATP molecule as well as the frequency of H-bonds between certain
> residues within the protein.
> My questions are as follows:
> 1) which flags should I use in g_hbond in order to obtain the above
> 2) how do I interpret the residues / atoms that form the  H-bond
> 3) When calculating H-bonds with gromacs, default values are donor-acceptor
> angle < 30 degrees and donor-acceptor distance is 0.35 nm (or 3.5
> angstrom).
> from what I read in the literature, the angle should be between 90-180
> degrees, thus < 90 degrees. Furthermore, some indicated that a cutoff of
> 0.39 nm includes within the hydrogen bonds also weaker h-bonds. What do you
> think should be the cutoff for both angle and distance for the above
> mentioned type of H-bonds?

Hi Vered,

Note that there ‘donor-acceptor angle’ is ambiguous. If you measure the hydrogen-donor-acceptor angle that should be ~< 30 degrees, whereas the donor-hydrogen-acceptor angle should be ~>120 degrees or so. Could this be the reason for the discrepancy with some of the literature?

Kind regards,

> Thanks a lot!
> Vered
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