One of the crucial design aspects of an organic photovoltaic device is the morphology of the active layer because it influences charge generation and transport. To better understand how to engineer desired morphologies in such devices we perform coarse-grained molecular dynamics simulations accelerated with graphics processing units. These simulations permit the molecular origins of 10-nanometer features to be observed over hundred-nanosecond time scales. We compare structures observed in our coarse-grained simulations with both experimental data and atomistic simulations through simulated diffraction experiments. We show how discrepancies between these structures are used to iteratively improve the coarse-grained models.