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

Vered Kunik vered at ofranlab.org
Wed Jan 7 17:09:20 CET 2015

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
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?

Thanks a lot!


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