Bad RMSD values from protein-ligand complex

[pelinsu]

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i have protein and ligand so I am using protein-ligand complex tutorial for MD. as well as I did molecular docking before to start MD. now

1. which complex should I use for MD, separately protein and ligand like protein-ligand complex or should I use directly docked complex from Autodock.
2. my first MD for 100 ns give me that bad RMSD values that is shown as following:
   
   

and I used “imx rms -s start.pdb -f md_0_10_center.xtc -n index.ndx -tu ns -o rmsd_jz4.xvg” scripts for backbone-backbone rmsd.
how I can improve my rmsd graph. it is not work.