Using QM/MM methods, we have simulated the action of a simple molecular machine, a cilium. It consists of a platform for surface Mounting; a photochemical motor unit, and a tail like effector that amplifies the small-scale conformational change of the motor unit into a larger scale beating motion usable for molecular transport. In this proof-of-principle application, we show that the techniques used here make it possible to perform such simulations within reasonable real time, if the device action is sufficiently fast. Additionally, we show that this molecular device actually works as intended for one isomerization direction. For the other direction, results are inconclusive, possibly because the total propagation times we can afford are too short to capture the complete event.