An important function of CONGEN is the evaluation and manipulation of the potential energy of a macromolecular system. Two types of manipulation are supported. First, one can minimize the energy by adjusting the coordinates of all the atoms in order to reduce its value. Several minimization algorithms are provided. Second, one can solve Newton's equations of motion using the potential energy in order to obtain a dynamics trajectory.
The commands which invoke these three types of manipulation are all parsed by the same routine, and any common actions are done therein.