Nowadays, by improving the abilities of computers molecular modeling has become a powerful technique in computational chemistry with ever-increasing practical interests. At the moment, using effective algorithms along with powerful processors enables us to simulate systems including thousands atoms up to several microseconds. However, finding a balance between the computational costs and reliable results still remains a challenge. Two general approaches help us to reveal the behavior of these systems: quantum mechanics and molecular dynamics calculations. Molecular dynamics (MD) studies the motion of a set of interacting atoms, molecules or particles. MD can extract experimental observables from the dynamics of the system by investigating the system motion.