A high speed rotary atomizer supported by active magnetic bearings (AMB) has been in service in a pharmaceutical-processing plant for over three years. This process challenges the AMBs by imposing variable, quasi-periodic external impulses on the atomizer. The impulses are occasionally large enough to overload the AMBs, resulting in backup bearing contact during operation. Implementation of a novel impulse detection and Impulse Recovery Compensator (IRC) introduced to allow continuous operation has been previously reported. In this work, a transient, nonlinear rotordynamic simulation of the atomizer, together with field measured position and current time histories, is used to help characterize the impulsive loads, the magnetic bearing control response and backup bearing reaction loads. The simulation results provide a reasonable match to field measured position and current time histories when the impulse load is produced by a sudden large unbalance, temporary or permanent. The simulation correctly predicts that amplifier saturation is relieved and the rotor re-levitates when the control is switched to the IRC. Predicted backup bearing loads during whirl are reasonable and subsequently calculated stress levels are consistent with favorable inspections of backup bearings removed from service. Future work with the simulation will include further improvements to the amplifier and backup bearing modelling.