Advances in computing technology have significantly increased the scientific interest in computer based molecular modeling of nano materials 1. In order to perform any computational study on molecular properties, it is necessary to create a molecular model. In other words, it is essential to create an accurate model of atomic interactions at the first step. This model could be used to investigate the mechanical properties of a material near molecular length scales 2. It can be derived by taking into account an appropriate crystal structure. Any technique that can produce a valid model for a given compound seems appropriate. Molecular modeling could be a useful tool at this stage. It is widely employed to determine molecular equilibrium structures. In addition, it could be used to design new materials with desirable properties 3. These theoretical methods can be classified into two board branch which are ��bottom up�� and ��top down��. ��Bottom up�� is based on quantum/molecular mechanics including the classical MD and ab initio methods. In contrast, ��top down�� approach arose from continuum mechanics. © 2016, Springer International Publishing Switzerland.