First-principles studies often rely on the assumption of equilibrium, which can be a poor approximation, e.g., for growth. Here, an effective chemical potential method for non-equilibrium systems is developed. A salient feature of the theory is that it maintains the equilibrium limits as the correct limit. In application to molecular beam epitaxy, rate equations are solved for the concentrations of small clusters, which serve as feedstock for growth. We find that the effective chemical potential is determined by the most probable, rather than by the lowest-energy, cluster. In the case of Bi2Se3, the chemical potential is found to be highly supersaturated, leading to a high nucleus concentration in agreement with experiment.