Understanding molecular simulation : from algorithms to applications

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This comprehensive guide explores the physics behind molecular simulation techniques essential for materials science. It addresses the challenges faced by computer simulators in selecting appropriate methods for specific applications, emphasizing the importance of understanding fundamental principles to enhance simulation efficiency. The text features pseudocode illustrations of simulation methods and practical case studies. Since the first edition, significant advancements in simulation techniques have emerged, prompting updates in this new edition. Key topics include transition path sampling for rare events, dissipative particle dynamics as a coarse-grained technique, and innovative methods for calculating long-range forces. It also covers Hamiltonian and non-Hamiltonian dynamics in constant-temperature and constant-pressure simulations, multiple-time step algorithms for constraints, defects in solids, and advanced sampling techniques for complex molecules. Additionally, parallel tempering for glassy Hamiltonians is discussed. New examples and questions have been incorporated to reflect recent applications, with case study codes available online. This edition assumes no prior knowledge of computer simulation, making it accessible to a broad audience.