A method for molecular dynamics (MD), Monte Carlo (MC), and energy minimization simulation utilizing a Hamiltonian that is divided into two parts is described. One part is treated with a quantum mechanical Hamiltonian, typically a small part of the simulated system that comprises the chromophore. The other part is treated with a classical mechanical Hamiltonian. This partitioning of the system allows us to simulate, for example, not only electronic spectroscopy but also chemical reactions when a bond is broken or to explore the excited state potential energy surface. The particular choice of the quantum mechanical Hamiltonian, the intermediate neglecting of differential overlap (INDO) model Hamiltonian, also offers the possibility of simulating systems that contain a transition metal, which only rarely have been accessible with traditional MD and MC methods. Test calculations on small systems are presented together with an investigation of the photophysics of uracil and 1,3-dimethyluracil.