Understanding Molecular Simulation, Second Edition: From Algorithms to Applications (Computational Science Series, Vol 1)

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When I have any question about simulations, this book is my first choice and it usually doesn't disappoint me. Best part of this book is crystal theory and algorithm. I know how to run a simulation, how to choose a parameter WITH CONFIDENCE after reading it. However, codes in it are not always helpful, I usually need to implement in my own way. In brief, this book is very good on basic principle and algorithm of molecular simulations, but not how to write a piece of code.

Understanding Molecular Simulation, Second Edition: From Algorithms to Applications (Computational Science Series, Vol 1) Overview

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.

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• Computer Simulation of Liquids
• Molecular Modelling: Principles and Applications (2nd Edition)
• Ab Initio Molecular Dynamics: Basic Theory and Advanced Methods
• Molecular Modeling and Simulation
• Statistical Mechanics

Molecular Modeling and Simulation: An Interdisciplinary Guide (Interdisciplinary Applied Mathematics)

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Molecular Modeling and Simulation: An Interdisciplinary Guide (Interdisciplinary Applied Mathematics) Overview

This book evolved from an interdisciplinary graduate course entitled Molecular Modeling developed at New York University. Its primary goal is to stimulate excitement for molecular modeling research while introducing readers to the wide range of biomolecular problems being solved by computational techniques and to those computational tools. The book is intended for beginning graduate students in medical schools and scientific fields such as biology, chemistry, physics, mathematics, and computer science. Other scientists who wish to enter, or become familiar, with the field of biomolecular modeling and simulation may also benefit from the broad coverage of problems and approaches. The book surveys three broad areas: biomolecular structure and modeling: current problems and state of computations; molecular mechanics: force field origin, composition, and evaluation techniques; and simulation methods: geometry optimization, Monte Carlo, and molecular dynamics approaches. Appendices featuring homework assignments, reading lists, and other information useful for teaching molecular modeling complement the material in the main text. Extensive use of world wide web resources is encouraged, and additional course and text information may be found on a supplementary website. Some praise for Tamar Schlick¿s ¿Molecular Modeling and Simulation: An Interdisciplinary Guide¿:||"The interdisciplinary structural biology community has waited long for a book of this kind which provides an excellent introduction to molecular modeling.¿|¿Harold A. Scheraga, Cornell University||"A uniquely valuable introduction to the modeling of biomolecular structure and dynamics. A rigorous and up-to-date treatment of the foundations, enlivened by engaging anecdotes and historical notes.¿|¿J. Andrew McCammon, Howard Hughes Medical Institute, University of California at San Diego||"I am often asked by physicists, mathematicians and engineers to recommend a book that would be useful to get them started in computational molecular biology. I am also often approached by my colleagues in computational biology to recommend a solid textbook for a graduate course in the area. Tamar Schlick has written the book that I will be recommending to both groups. Tamar has done an amazing job in writing a book that is both suitably accessible for beginners, and suitably rigorous for experts.¿|¿J.J. Collins, Boston University

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