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The extremely powerful technique of molecular dynamics simulation involves solving the classical many-body problem in contexts relevant to the study of matter at the atomistic level. Since there is no alternative approach capable of handling this extremely broad range of problems at the required level of detail, molecular dynamics methods have proved themselves indispensable in both pure and applied research. This book, first published in 2004, is a blend of tutorial and recipe collection, providing both an introduction to the subject for beginners and a reference manual for the more experienced practitioner. It is organized as a series of case studies that take the reader through each of the steps from formulating the problem, developing the necessary software, and then using the programs to make actual measurements. The second edition of the book includes a substantial amount of new material as well as completely rewritten software.

Provides hands-on knowledge enabling students of and researchers in chemistry, biology, and engineering to perform molecular simulations This book introduces the fundamentals of molecular simulations for a broad, practice-oriented audience and presents a thorough overview of the underlying concepts. It covers classical mechanics for many-molecule systems as well as force-field models in classical molecular dynamics; introduces probability concepts and statistical mechanics; and analyzes numerous simulation methods, techniques, and applications. Molecular Simulations: Fundamentals and Practice starts by covering Newton's equations, which form the basis of classical mechanics, then continues on to force-field methods for modelling potential energy surfaces. It gives an account of probability concepts before subsequently introducing readers to statistical and quantum mechanics. In addition to Monte-Carlo methods, which are based on random sampling, the core of the book covers molecular dynamics simulations in detail and shows how to derive critical physical parameters. It finishes by presenting advanced techniques, and gives invaluable advice on how to set up simulations for a diverse range of applications. -Addresses the current need of students of and researchers in chemistry, biology, and engineering to understand and perform their own molecular simulations -Covers the nitty-gritty ? from Newton's equations and classical mechanics over force-field methods, potential energy surfaces, and probability concepts to statistical and quantum mechanics -Introduces physical, chemical, and mathematical background knowledge in direct relation with simulation practice -Highlights deterministic approaches and random sampling (eg: molecular dynamics versus Monte-Carlo methods) -Contains advanced techniques and practical advice for setting up different simulations to prepare readers entering this exciting field Molecular Simulations: Fundamentals and Practice is an excellent book benefitting chemist, biologists, engineers as well as materials scientists and those involved in biotechnology.

Molecular dynamics simulation is a significant technique to gain insight into the mechanical behavior of nanostructured (NS) materials and associated underlying deformation mechanisms at the atomic scale. The purpose of this book is to detect and correlate critically current achievements and properly assess the state of the art in the mechanical behavior study of NS material in the perspective of the atomic scale simulation of the deformation process. More precisely, the book aims to provide representative examples of mechanical behavior studies carried out using molecular dynamics simulations, which provide contributory research findings toward progress in the field of NS material technology.

Ab initio molecular dynamics revolutionized the field of realistic computer simulation of complex molecular systems and processes, including chemical reactions, by unifying molecular dynamics and electronic structure theory. This book provides the first coherent presentation of this rapidly growing field, covering a vast range of methods and their applications, from basic theory to advanced methods. This fascinating text for graduate students and researchers contains systematic derivations of various ab initio molecular dynamics techniques to enable readers to understand and assess the merits and drawbacks of commonly used methods. It also discusses the special features of the widely used Car–Parrinello approach, correcting various misconceptions currently found in research literature. The book contains pseudo-code and program layout for typical plane wave electronic structure codes, allowing newcomers to the field to understand commonly used program packages and enabling developers to improve and add new features in their code.

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.

On May 21-24, 1997 the Second International Symposium on Algorithms for Macromolecular Modelling was held at the Konrad Zuse Zentrum in Berlin. The event brought together computational scientists in fields like biochemistry, biophysics, physical chemistry, or statistical physics and numerical analysts as well as computer scientists working on the advancement of algorithms, for a total of over 120 participants from 19 countries. In the course of the symposium, the speakers agreed to produce a representative volume that combines survey articles and original papers (all refereed) to give an impression of the present state of the art of Molecular Dynamics. The 29 articles of the book reflect the main topics of the Berlin meeting which were i) Conformational Dynamics, ii) Thermodynamic Modelling, iii) Advanced Time-Stepping Algorithms, iv) Quantum-Classical Simulations and Fast Force Field and v) Fast Force Field Evaluation.