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Abstract— This research aims to study the dynamic modelling of experimental manipulator rig underwater condition. The experimental manipulator has been used as a single link pipe derived by motor to monitor the pipe angles under disturbance water. After studying the output system previously for manipulator hub-angle and vibration, Flower pollination method (FPM) employed to predict and model the dynamic behavior as a transfer function after collecting the motor torque as an input data and hub-angle only due to little affection of the vibration underwater compared with the hub-angle. However, many types of testing methods have been implemented to validate of proposed method; which are stability, correlation tests and Mean square error (MSE) methods. As a result, FPM has been performed as a good prediction to model the system as a transfer function based on number of model order. Whereas, the best model order has been noticed are 3rd model order for FPM that recorded lowest MSE of 1.23021×10-4 and 1.72250×10-4 for modelling and validating respectively.