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This research investigates the effect of the groove depth, a design variable of fluid dynamic bearings (FDBs), and the shaft diameter, a structural design variable of a hard disk drive (HDD) on the dynamics of a HDD spindle system. The flying height of the HDD spindle system is determined by using the static analysis of the FDBs. The stiffness and damping coefficients are calculated by using the dynamic analysis of the FDBs. The free vibration characteristics and shock response of the HDD spindle system are analyzed by using the finite element method and the mode superposition method. An experimental modal test is also performed to verify the accuracy of the proposed method. This research shows that the shaft diameter changes the rocking frequencies in wider range than the groove depth of FDBs and that the shock response of a HDD spindle system is affected by the groove depth of FDBs. It also shows that the stiffness coefficients of journal bearing affect the rocking frequencies because their magnitudes are within the range of the stiffness of the supporting structure and that the damping coefficients of thrust bearing affect the axial frequency because the stiffness of thrust bearing is much smaller than that of the supporting structure.