This book will be beneficial for students, researchers and scientists working in the field of molecular dynamics simulation. In this book, Materials Studio software developed by Accelrys, a software company headquartered in the United States, has been used for performing the simulations and analysis. The source codes written in the book can be used by any one for modeling. The book starts with an introduction to molecular dynamics. Then various molecular dynamics methods will be discussed in detail. As the book progresses, various case studies related to modeling of composites at nano level will be discussed. The properties predicted are mechanical, thermal, optical and electrical. The concept of perl scripting has also been discussed in detail. Lastly the applications of molecular dynamics in various fields of engineering and technology will be discussed. The nanocomposite materials discussed in this book include polymer-matrix composites. The reinforcements used are carbon nanotubes, graphene, nanoparticles and nanofibers.