A system and method for controlling bending modes of a rotor assembly is disclosed. The rotor assembly can be supported by one or more bearings in an integrated machine. The method can include accelerating the rotor assembly to a first rotational speed via a first torsional force applied to the drive shaft and then removing the first torsional force. The method can also include obtaining first measurements of the rotational speed and frequency of one or more bending modes of the rotor assembly during a first rotary machine coast down period from the first rotational speed. The process can be repeated to determine a relationship between rotational speed, bending mode frequency, and gain. The one or more bearings can then be controlled based on the measurements and the relationship. The system can have one or more processors or controllers to implement the method.