The Art of Molecular Dynamics Simulation is a comprehensive guide to the technique of molecular dynamics (MD) simulation, which is used to study matter at the atomic level. This second edition of the book has been extensively revised and expanded, adding new material and completely rewriting the software used in the case studies. The book is designed as a blend of tutorial and recipe collection, providing an introduction for beginners and a reference manual for experienced practitioners. It is organized as a series of case studies that guide the reader through the process of formulating problems, developing software, and using programs to make measurements. Dennis C. Rapaport, a professor of physics at Bar-Ilan University, is the author of the book. He has a background in physics and has been involved in computer modeling since his undergraduate years. His research interests include the methodology of molecular dynamics simulation and its applications in various fields. The book covers a wide range of topics, including basic molecular dynamics, simulating simple systems, equilibrium and dynamical properties of simple fluids, alternative ensembles, nonequilibrium dynamics, rigid and flexible molecules, geometrically constrained molecules, internal coordinates, many-body interactions, long-range interactions, step potentials, time-dependent phenomena, granular dynamics, algorithms for supercomputers, more about software, and the future of molecular dynamics simulation. The book is structured to provide both an introduction to the subject and a reference for more experienced practitioners. It includes case studies that take the reader through each step of the process, from problem formulation to the presentation of results. The book also includes a variety of computational techniques and methods, but not all combinations of methods and problems are covered. The software used in the case studies has been completely rewritten to reflect a more modern programming style. The book is intended to be used as a cookbook, with the hope that readers can use the case studies to achieve both the goals of an introduction and a reference manual. The book is written for readers with some familiarity with classical and statistical mechanics, numerical methods, and computer programming. The software described in the book is available for download for personal, non-commercial use. The programs are provided for educational purposes only and are not warranted to be free from error or suitable for particular applications.The Art of Molecular Dynamics Simulation is a comprehensive guide to the technique of molecular dynamics (MD) simulation, which is used to study matter at the atomic level. This second edition of the book has been extensively revised and expanded, adding new material and completely rewriting the software used in the case studies. The book is designed as a blend of tutorial and recipe collection, providing an introduction for beginners and a reference manual for experienced practitioners. It is organized as a series of case studies that guide the reader through the process of formulating problems, developing software, and using programs to make measurements. Dennis C. Rapaport, a professor of physics at Bar-Ilan University, is the author of the book. He has a background in physics and has been involved in computer modeling since his undergraduate years. His research interests include the methodology of molecular dynamics simulation and its applications in various fields. The book covers a wide range of topics, including basic molecular dynamics, simulating simple systems, equilibrium and dynamical properties of simple fluids, alternative ensembles, nonequilibrium dynamics, rigid and flexible molecules, geometrically constrained molecules, internal coordinates, many-body interactions, long-range interactions, step potentials, time-dependent phenomena, granular dynamics, algorithms for supercomputers, more about software, and the future of molecular dynamics simulation. The book is structured to provide both an introduction to the subject and a reference for more experienced practitioners. It includes case studies that take the reader through each step of the process, from problem formulation to the presentation of results. The book also includes a variety of computational techniques and methods, but not all combinations of methods and problems are covered. The software used in the case studies has been completely rewritten to reflect a more modern programming style. The book is intended to be used as a cookbook, with the hope that readers can use the case studies to achieve both the goals of an introduction and a reference manual. The book is written for readers with some familiarity with classical and statistical mechanics, numerical methods, and computer programming. The software described in the book is available for download for personal, non-commercial use. The programs are provided for educational purposes only and are not warranted to be free from error or suitable for particular applications.