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Understanding Molecular Simulation: From Algorithms to Applications explains the physics behind the "recipes" of molecular simulation for materials science. Computer simulators are continuously confronted with questions concerning the choice of a particular technique for a given application. A wide variety of tools exist, so the choice of technique requires a good understanding of the basic principles. More importantly, such understanding may greatly improve the efficiency of a simulation program. The implementation of simulation methods is illustrated in pseudocodes and their practical use in the case studies used in the text.
Since the first edition only five years ago, the simulation world has changed significantly -- current techniques have matured and new ones have appeared. This new edition deals with these new developments; in particular, there are sections on:
- Transition path sampling and diffusive barrier crossing to simulaterare events
- Dissipative particle dynamic as a course-grained simulation technique
- Novel schemes to compute the long-ranged forces
- Hamiltonian and non-Hamiltonian dynamics in the context constant-temperature and constant-pressure molecular dynamics simulations
- Multiple-time step algorithms as an alternative for constraints
- Defects in solids
- The pruned-enriched Rosenbluth sampling, recoil-growth, and concerted rotations for complex molecules
- Parallel tempering for glassy Hamiltonians
Examples are included that highlight current applications and the codes of case studies are available on the World Wide Web. Several new examples have been added since the first edition to illustrate recent applications. Questions are included in this new edition. No prior knowledge of computer simulation is assumed.
List of contents
1. Introduction
Part I Basics
2. Statistical Mechanics
3. Monte Carlo Simulations
4. Molecular Dynamics Simulations
Part II Ensembles
5. Monte Carlo Simulations in Various Ensembles
6. Molecular Dynamics in Various Ensembles
Part III Free Energies and Phase Equilibria
7. Free Energy Calculations
8. The Gibbs Ensemble
9. Other Methods to Study Coexistence
10. Free Energies of Solids
11. Free Energy of Chain Molecules
Part IV Advanced Techniques
12. Long-Range Interactions
13. Biased Monte Carlo Schemes
14. Accelerating Monte Carlo Sampling
15. Tackling Time-Scale Problems
16. Rare Events
17. Dissipative Particle Dynamics
Report
".brilliantly maintains a balance between explaining the physical phenomena and performing computations. Its marvelous writing style invites scientists and students to deepen their knowledge of MD simulations." --ComputingReviews.com, January 11, 2013
"... this book brilliantly lays down the scientific foundations of the simulational approach ..." --Prof. Kurt Binder in Physics World, 1997
"... a treasure. The book is a marvellous mix of just enough formalism with an informal and readable style, sufficient detail to understand methodological advances, appropriate mathematics ..." --Prof. Mark A. Ratner in Physics Today, 1997
