A system includes an electronic power converter and a controller. The electronic power converter supplies power to one or more motor drives of an HVAC and/or refrigeration system. The controller obtains a plurality of pulse width modulation (PWM) algorithms. Each PWM algorithm has an associated harmonic signature. The controller further determines one or more resonance frequencies associated with the HVAC and/or refrigeration system. The controller also selects a first PWM algorithm from the plurality of PWM algorithms based at least in part on the harmonic signature associated with the first PWM algorithm mitigating the one or more resonance frequencies associated with the refrigeration system. The controller further operates the electronic power converter according to the first PWM algorithm.