Nanoscopic problems on the cathode catalyst layer in proton exchange membrane fuel cells are highly important to evaluate the performance of the devices. The aim of this work is to suggest a proper potential model for molecular dynamics simulation to deal with this problem. Four potential models TIP3P, TIP4P, TIP5P and NvE model are numerically validated and compared with experimentation. The NvE model shows good agreement with measurement, while it is the time-consuming model. This research is carrying out a complex system which describes the simplified cathode catalyst layer by applying the NvE model.