This book was conceived as a result of many years research with students and postdocs in molecular simulation, and shaped over several courses on the subject given at the University of Groningen, the Eidgen¨ossische Technische Hochschule (ETH) in Z¨urich, the University of Cambridge, UK, the University of Rome (La Sapienza), and the University of North Carolina at Chapel Hill, NC, USA. The leading theme has been the truly interdisciplinary character of molecular simulation: its gamma of methods and models encompasses the sciences ranging from advanced theoretical physics to very applied (bio)technology, and it attracts chemists and biologists with limited mathematical training as well as physicists, computer scientists and mathematicians