Recently, providing a model in order to investigate human body vibrations and also finding a methodology to simulate the functionality of central nervous system in muscle tuning while pre and post fatigue conditions during running has been discussed in numerous papers. In the current study, a 4 degree of freedom vibration model of human body and an objective function that mimics the functionality of central nervous system with bounds for pre-fatigue and post fatigue conditions were considered. Firstly, it was shown that the optimization method used in the literature leads to inaccurate results. Then, in order to achieve more accurate results, the optimization problem was solved using Particle Swarm Optimization method. A comparison between the results of current study with those in literature showed that our results are more consistent with experiments. Our findings indicated that an increase in running time followed by an increase in fatigue leads to a significant decrease in the safe region and increase in vibration amplitude of lower body wobbling mass. Moreover, a parametric study was conducted to investigate the effects of mass distribution and variations in touchdown velocities on the area of the safe region for both pre and post fatigue conditions. A high dependency of this area to the mass distribution and touchdown velocities of lower extremities was also indicated. The results of this study can be useful in the shoe design for running and similar activities.