Active magnetic bearings present a technology that has many advantages compared to traditional bearing concepts. Active magnetic bearings, however, require retainer bearings in order to prevent damages in the event of a component, power, or a control system failure. In the drop-down, when the rotor drops from the magnetic field on the retainer bearings, the design of the retainer bearings has a significant influence on the dynamic behavior of the rotor. In this study, the dynamics of an active magnetic bearing supported rotor during the drop on retainer bearings is studied employing a simulation model. The retainer bearings are modeled using a detailed ball bearing model while the flexibility of the rotor is described using the finite element method with component mode synthesis. The model is verified by comparing measurements carried out using an existing test rig and simulation results. In this study, the verified simulation model is employed studying the effect of misalignment of retainer bearings during the rotor drop-down on the retainer bearings. It is concluded in this study that the misalignment of the retainer bearings is harmful and can lead to whirling motion of the rotor.