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The paper proposes a control scheme for detecting and compensating the low-frequency vibrations in hard disk drive systems. A vibration detector is proposed, utilizing the down-sampled position error signal (PES). Due to the performance limitation in loop shaping, attenuating low-frequency vibration is usually penalized by high frequency disturbance amplification. This paper proposes an adaptive scheme to intelligently adjust a vibration reduction factor, such that when vibration level is low, the servo loop maintains its normal operation mode, and little or no compensation is carried out. Experiments on hard disk drives on a vibration shaker validated the effectiveness of the proposed compensation scheme.