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

Justin Lemkul jalemkul at vt.edu
Wed Jan 7 17:55:46 CET 2015

On 1/7/15 11:08 AM, Vered Kunik 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

What you're looking to do is straightforward application of g_hbond without any 
special flags.  You may want special index groups to define specific residues or 
moieties.  All of this is covered in the manuals.

> 2) how do I interpret the residues / atoms that form the  H-bond

If you use index groups, it should be straightforward.  Otherwise, export -hbn 
to map all the groups.

> 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?

90 degrees seems a bit unusual; beware of different conventions for the order of 
the atoms in those definitions.  The widest range I usually see is 120-180 
degrees.  I also doubt there is much of a practical difference between 0.35 and 
0.39, but it's certainly easy to do and compare.  You'll have an answer in moments.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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