Ion channels control the flow of ions across the membrane in all cells. It is an integral membrane protein. In this study molecular dynamics simulation and principal component analysis of the NaK ion channel in water environment have been performed. From the analysis of the simulation trajectory, it is observed that flexibility presents in the each helixes. RMSF values are seen to be largest in case of the N-terminal residues of B chain which are the part of M0 helix. It is also seen that the filter shows considerable fluctuation, and it does not act as a rigid tube through which selected ions pass.