The scheme of motion analysis using the Free-running system is suggested in this study. Gyropilot is carried out to control the bow angle. The thrust and circular frequency of propeller shaft is controlled to maintain the constant speed. Movement of a model ship in the tank is measured by using an optical tracking system. To analyze ship motion numerically, added masses, damping coefficients and wave exciting forces are calculated by a 3-Dimensional panel method in terms of translating oscillatory Green functions in the frequency domain. Equations of motion considering the memory effect are numerically solved by Newmark-beta method in the time domain.