The accurate treatment of non-bonded interactions is paramount in a force field descrip­tion. The philosophy behind the AMBER force field is to deal with these interactions in the most accurate way possible within the limitations of the available hardware. Non-bonded interactions do not depend upon a specific bonding relationship between atoms. They are “through-space” interactions, the number of which scales roughly as the square of the num­ber of atoms. Unsurprisingly, the non-bonded interactions form the most time-consuming component of molecular mechanics simulations. Molecular mechanics force fields typically consider the non-bonded interactions as two groups, one comprising electrostatic interac­tions and the other van der Waals interactions.

8.2.2.4.1 ELECTROSTATIC INTERACTIONS

The last term in Equation (8.3) describes the electrostatic interactions within the system. There are a number of ways to represent the charge distribution within a molecule, the simplest being the use of point charges. This is the method utilized by most biologically oriented force fields. In the point charge model a series of fractional charges are distributed throughout the molecule. If the charges are centered on atoms then they are referred to as partial atomic charges. The interaction energy is calculated using Coulomb’s law.

Since the charge on an atom is not experimentally observable the partial atomic charges have to be assigned in an analogous fashion to the parameters used in the bonding interaction terms. The partial charges are generally obtained by fitting to a charge potential obtained from an ab initio electronic structure calculation.

Separation