You can do it using VMD trajectory analysis tools. Follow this link: http://www.ks.uiuc.edu/Training/Tutorials/science/timeline/tutorial_timeline-html/node4.html

And once you have generated the graphs shown there, you can integrate that residue-wise or time-wise to get those percentages in Mathematica or IPython.

try using 'hbond' and 'mindist' commands in gromacs

Hi,

Using gmx make_ndx you can create an appropriate index group containing the residues you would like to monitor. You can then use gmx bond, passing in the index group created earlier to calculate the prevalence of the hydrogen bonds. 

Thank you all.