In 1959, physicist Richard Feynman gave a historical lecture “There’s Plenty of Room at the Bottom”. By ‘maneuvering things atom by atom’, he envisioned building smaller and smaller machines, and ultimately using these to build machines at the smallest possible scale. Even after sixty years, the exciting field of nanotechnology is exploding. Over the last few decades, extensive research has been carried out at the atomic scale of matter. Owing to enormous development in high performance computing, computational nanotechnology has exploded in recent years. Because of this, several computing algorithms have been widely used e.g. Monte Carlo Methods (MC), Kinetic Monte Carlo Methods (KMC), and Molecular Dynamics (MD). LAMMPS (“Large-scale Atomic/Molecular Massively Parallel Simulator”), developed by Sandia National Laboratories, has been the ubiquitous for research involving MD. In this book, we have explored some very important and basic problems of Molecular Simulations. All the problems discussed in this book are very fundamental and will develop a strong foundation for advanced research.