Motion disorders pose a significant global health concern and are often managed with pharmacological treatments that may lead to undesirable long-term effects. Current therapeutic strategies lack differentiation between healthy and unhealthy muscles in a patient, necessitating a targeted approach to distinguish between musculature. There is still no motion analyzer application for this purpose. Additionally, there is a deep gap in motion analysis software as some studies prioritize simulation, neglecting software needs, while others concentrate on computational aspects, disregarding simulation nuances. We introduce a comprehensive five-phase methodology to analyze the neuromuscular system of the lower body during gait. The first phase employs an innovative IoT-based method for motion signal capture. The second and third phases involve an agent-driven biomechanical model of the lower body skeleton and a model of human voluntary muscle. Thus, using an agent-driven approach, motion-captured signals can be converted to neural stimuli. The simulation results are then analyzed by our proposed ensemble neural network framework in the fourth step in order to detect abnormal motion in each joint. Finally, the results are shown by a userfriendly graphical interface which promotes the usability of the method. Utilizing the developed application, we simulate the neuromusculoskeletal system of some patients during the gait cycle, enabling the classification of healthy and pathological muscle activity through joint-based analysis. This study leverages cloud computing to create an infrastructure-independent application which is globally accessible. The proposed application enables experts to differentiate between healthy and unhealthy muscles in a patient by simulating his gait.