The parameter phi can be used to synchronize the torsional potential to the initial rotameric state of the molecule whose energy is being computed. The non-bonded energy accounts for repulsion, van der Waals attraction, and electrostatic interactions. Repulsion occurs when the distance between interacting atoms becomes even slightly less than the sum of their contact radii. The electrostatic contribution is modeled using a Coulombic potential. Often, the molecular dielectric is set to a constant value between 1.0 and 5.0.
Some programs assign charges using rules or templates, especially for macromolecules.
Use of a different method can invalidate the force-field consistency.