Some embodiments of the present invention provide a system that controls a device that generates vibrations in a computer system. During operation, a critical vibration frequency is determined for the computer system. Next, a keep-out zone is generated based on the critical vibration frequency, wherein the keep-out zone specifies a range of frequencies to be avoided. Then, the device is controlled based on the keep-out zone to reduce vibrations generated by the device in the keep-out zone.