1. A system for performing molecular mechanics calculations for a molecular system, comprising: a programmable logic device configured to compute a non-bonded energy term for atoms within a molecular system without tests to detect and skip atom pairs that are within a predefined number of bonds from one another and without tests to detect and weight such atom pairs; and a computational system, coupled to the programmable logic device, for computing a nearby non-bonded energy correction term for atoms that are within the predefined number of bonds from one another, and correcting the non-bonded energy term with the nearby non-bonded energy correction term to generate a total non-bonded energy for the molecular system.