Hydrogen bonding distribution in molecular dynamics simulation in gromacs?

09 September 2017 0 953 Report

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

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