Special purpose vessels such as drillship and ocean research vessels install the DPS(Dynamic Positioning System) to maintain the position and heading for long-time operation. This paper deals with the design parameters for the control theory and filter algorithms of DP system. for the environmental loadings wind forces, current forces and wave forces were considered. In order to estimate the low frequency motions without first-order wave motion, the Kalman filter was used and it was assumed that the first-order wave forces correspond to system noises and first-order wave motions are measurement noises. In this simulation, the length of research vessel is 65 meters and it has four thrusters to maintain the position. The ability of keeping position and heading was confirmed. For the calculation of thruster input the LQR and LOI control theory were adopted and the effects of gain were investigated.