FIGURE 1.

The set of interactions that are the molecular mechanics paradigm that defines the forces that drive the motion of atoms in a molecular dynamics simulation with all atom resolution. The bond, angle and dihedral potentials are the intramolecular interactions that define molecule structure and the interactions between covalently bound atoms. Each atom has a partial charge that interacts with all other atoms through electrostatic forces to model electronegativity and H-bonding behavior; short range attractive and repulsive forces due to the Van-der-Waals and Pauli Exclusion Principle, respectively, are modeled through the Lennard-Jones interaction.