Drug development is a tedious process which requires a tremendous time and money investment. The "lock-and-key" model of ligands binding to frozen, rigid receptors has led to several false positives and false negative in drug screening. This book introduced how Molecular Dynamics simulations have improved the in silico drug discovery stage by providing us a thorough understanding of motions and flexibility of targeted proteins Readers will be equipped with several techniques in Molecular Dynamics simulations in details from basic concept to application. Case studies for computer aided drug design against influenza A viruses were also illustrated in detail.