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With a growing penetration of Permanent Magnet Synchronous Wind Turbine Generations (PMSG-WT) into the modern power system, a comprehensive modeling and analysis of PMSG-WT is required to investigate its dynamic stability and interaction between large wind farm and power grids. In this work, a complete detailed MW-class variable speed Wind Turbine System based on a Permanent Magnet Synchronous Generator and a full-scale IGBT Voltage Source Converter is developed for PSCAD/EMTDC simulation study. This control scheme comprises both the mostly applied Maximum Point Power Tracking Operation and Double PWM active/reactive power independent control strategy. Moreover, a DC-link over-voltage protection scheme is designed and implemented in this model. A two mass drive train model is integrated into this WT model to achieve a reasonably accurate simulation on the transient stability of PMSG-WT. The feasibility of the established PMSG-WT physical model plus the effectiveness of proposed control and protection scheme are evaluated through a series of simulation studies under both variable wind speed conditions and a three-phase grid disturbance. Simulation results demonstrate that the PMSG-WT model possesses desirable capabilities of operation at the maximum power point as well as enhanced Low Voltage Ride Through Function (LVRT).