I'm currently doing a MD simulation of a specific protein, as well as trying to understand its interaction with a specific ligand. As for my progress, I'm already done in determining the conformations of my protein and about to dock it with my ligand. However, aside from the binding energy, I would also like to determine the changes in RMSD value of my protein residue upon it's interaction with my ligand as it may led me to elucidating the impact of my ligand to my receptor.