A method, medium, and apparatus controlling a hard disk drive, and more particularly, a method, medium, and apparatus controlling a track seek of a hard disk drive, where the hard disk drive compensates for a gain distortion and a phase delay caused by a notch filter and a VCM driver using a sinewave acceleration trajectory. According to the method of controlling a track seek of a hard disk drive, an ideal sinewave for obtaining a position y*(n), a velocity v*(n), and an acceleration a*(n), according to a sinewave acceleration trajectory, and a sinewave indicating a gain distortion and a phase delay may be integrated and a VCM driving current u(n) can be generated by the integrated sinewave for compensating for gain distortion and phase delay, compensating for a value C(j2.pi.f) of the gain distortion and the phase delay caused by the notch filter and the VCM driver.