Hi,
I have run the MD of a protein by using Gromacs.
I have generate the number of hydrogen bonds between protein and ligand by following command:-
gmx hbond -f md_0_1.xtc -s md_0_1.tpr -num trp_hnum.xvg -ac hbac.xvg -dist hbdist.xvg -ang hbang.xvg -hbn hbond.ndx -hbm hbmap.xpm
I got almost 4 hydrogen bond numbers between protein and ligand throughout the simulation.
However, i got a range of 10 to 16 hydrogen bond numbers in range of 2.6 to 3.5 A from hbdist.xvg.
I want to know how can i relate these 10 to 16 hydrogen bonds distributions from hydrogen bond results (4 hydrogen bonds)?
Thank you