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

Daan Frenkel (Author), Berend Smit (Author)

Book Description

ISBN-10: 0122673514 | ISBN-13: 978-0122673511 | Publication Date: November 7, 2001 | Edition: 2

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.

Editorial Reviews

Review

"... 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

From the Back Cover

This book explains the physics behind the "recipes" of molecular simulation for materials science. Computer simulators are continously confronted with questions concerning the choice of a particular technique for a given application. Since a wide variety of computational tools exists, 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. Examples are included that highlight current applications, and the codes of the case studies are available on the World Wide Web. No prior knowledge of computer simulation is assumed. --This text refers to an out of print or unavailable edition of this title.

See all Editorial Reviews

Product Details

• Hardcover: 664 pages
• Publisher: Academic Press; 2 edition (November 7, 2001)
• Language: English
• ISBN-10: 0122673514
• ISBN-13: 978-0122673511
• Product Dimensions: 9.4 x 5.6 x 1.6 inches
• Shipping Weight: 2.2 pounds (View shipping rates and policies)
• Average Customer Review: 4.3 out of 5 stars  See all reviews (12 customer reviews)
• Amazon Best Sellers Rank: #50,474 in Books (See Top 100 in Books)
  • #2 in Books > Professional & Technical > Professional Science > Chemistry > Molecular Chemistry
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Customer Reviews

Most Helpful Customer Reviews

22 of 22 people found the following review helpful:

5.0 out of 5 stars A great book for begginers., May 16, 1999

By 

[e-mail] (Mexico City.) - See all my reviews

This review is from: Understanding Molecular Simulation: From Algorithms to Applications (Hardcover)

This book covers many interesting topics in molecular simulation, both Monte Carlo and M.D. It focuses on understanding the main ideas rather than giving long codes. It's a good place to start, but it also covers some ideas not found in many other books. When I try to extend my molecular dynamics program I always check what Frenkel and Smit have to say about it.

32 of 35 people found the following review helpful:

4.0 out of 5 stars A nice disappointment, August 30, 2001

By 

Jose R. Valverde Carrillo "jrvalverde" (EMBnet/CNB, Madrid Spain) - See all my reviews

This review is from: Understanding Molecular Simulation: From Algorithms to Applications (Hardcover)

The title of the book is overly ambitious and falls short on its promises. The book is a good introduction to Molecular Mechanics (MM), Molecular Dynamics (MD) and Monte Carlo (MC) methods, with detailed descriptions of the methods used and FORTRAN (pseudo)code, covering from the basics to some middle-level and some advanced algorithms.
But it does NOT cover all the fields of Molecular Modelling, just the three mentioned (MM, MD and MC), there's no coverage of quantum mechanics methods, nor QSAR or other technologies. And, while it described the algorithms, I can't think of it going all the way through up to building applications. For this, Rapaport's makes a better job, and for a general intro to Molecular Modelling, Grant & Richards' Computational Chemistry is more comprehensive (albeit at a more superficial level). Nor does it provide much detail on the methods used in modelling biological macromolecules, an increasing application field for the methods discussed in the book.
All in all, this book fails to satisfy its cover title, it won't introduce to the whole field (just the areas of MM, MD and MC) nor does it go up to application level. But it IS a REAL GOOD introduction to the subjects covered and their basic algorithms,
with sample code, detailed descriptions and plenty of references to specialized articles, texts and resources.

20 of 21 people found the following review helpful:

5.0 out of 5 stars Perfect for New Grad Students, November 23, 2002

By 

Owen Hehmeyer (Princeton, NJ) - See all my reviews
(REAL NAME)   

This review is from: Understanding Molecular Simulation, Second Edition: From Algorithms to Applications (Computational Science Series, Vol 1) (Hardcover)

This book is how I bootstrapped my way into being a molecular simulationist. Anyone who can program in some language can get started writing simple routines for the basic MD and MC simulations.

I do Monte Carlo simulations at Princeton, and found this book to be the most helpful available for getting my research started. It is my most common reference, and is used extensively in writing background information for various research documents.

However, after you have written your first few codes, you will pass the level of this book and need to move on. I use it less now than I did my first year.

Every student in my group (Panagiotopoulos) has this book I think. And like me, they started with it, but moved on.