ABSTRACT
This chapter discusses molecular dynamics, its pros and cons and various other methods alternative to classical molecular dynamics simulations that are used to study complex biological phenomenon. Forcefields would lay foundation to understand the concept of computing free energies using molecular dynamics, and quantum mechanics and semiempirical methods would throw light on how forcefield parameters are developed for any chemical system. The chapter also discusses statistical mechanics that would lay foundation in making attempts relating microscopic state to macroscopic states, and explaining various ensembles in computer simulations and importance of Ergodic hypothesis. Quantum Mechanics was seen as a competitive technique to molecular mechanics as both the methods were developed by different group-seeking answer to different questions revolving around molecular modeling. A molecule or biomolecular system as a whole has certain energy at a given coordinate space depending on its position on the potential energy surface (PES).
