Computational molecular modeling and simulation approaches have become very powerful tools that can be used to predict and investigate atomic structure, geometrical and electronic properties, binding energies, charge transfer, interactions between molecules, hydration structure, etc. The two most common models that are used in the molecular modeling and simulation are quantum mechanics and molecular mechanics. The choice of technique depends on the conditions such as desired properties of molecules, reliable results comparing with the experimental results, the length and time scales of interested systems, availability of computer resources for calculations, etc. In general, a few tens to hundreds of atoms are very accurately simulated with quantum mechanics methods, wherein the simulations are aimed toward the solution of the complex quantum many-body Schrödinger equation of the atomic system (including nuclei and electrons), using numerical algorithms. For larger size systems (hundreds of thousands of atoms), classical atomistic or molecular dynamic (MD) simulations, which refer most commonly to the situation wherein the motion of atoms or molecules is treated using approximate finite difference equations of Newtonian mechanics are used.
See Molecular Simulation Center Point (Thailand) at http://nanotech.sc.mahidol.ac.th/simulation/index.html