Forces are contributed both through pair wise non-bonded interactions for all atom pairs i and j (red text in Eq. 1) and multibody terms that describe the bonded interaction for bonded atoms in the system (blue text in Eq. 1). Note that Eq. 1 features many elements that are parameterized not to vary with atomic position, such as equilibrium bond lengths (b 0 ), partial atomic charges (q) and other similar terms that constitute the force field. These parameters are available for many small molecules using the CHARMM general force field, which uses quantum mechanical target data for related compounds to determine by analogy parameters for similar molecules. When analogous topologies have not been previously parameterized in the general force field, optimization of the interaction parameters encoded by Eq. 1 is required.