"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; and, 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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".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
From the Author
Understanding Molecular Simulations
The book is aimed at readers who are active in computer simulation, orare planning to become so. Computer simulators are continuously confronted with questions concerning the choice of technique, because there is a bewildering variety of computational tools available. We believe that, in order to make a rational choice, a good understanding of the physics behind each technique is essential. Our aim is to provide the reader with this background. --This text refers to an out of print or unavailable edition of this title.
The book is aimed at readers who are active in computer simulation, orare planning to become so. Computer simulators are continuously confronted with questions concerning the choice of technique, because there is a bewildering variety of computational tools available. We believe that, in order to make a rational choice, a good understanding of the physics behind each technique is essential. Our aim is to provide the reader with this background. --This text refers to an out of print or unavailable edition of this title.
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First Sentence
It usually takes decades rather than years before a fundamentally new invention finds widespread application. For computer simulation, the story is rather different. Read the first page
Front Cover | Copyright | Table of Contents | Excerpt | Index
It usually takes decades rather than years before a fundamentally new invention finds widespread application. For computer simulation, the story is rather different. Read the first page
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Front Cover | Copyright | Table of Contents | Excerpt | Index
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Most Helpful Customer Reviews
3 of 3 people found the following review helpful
By A Customer
Format: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.
Most Helpful Customer Reviews on Amazon.com (beta)
Amazon.com:
4.3 out of 5 stars
12 reviews
35 of 38 people found the following review helpful
4.0 out of 5 stars
A nice disappointment
30 Aug 2001
By Jose R. Valverde Carrillo
- Published on Amazon.com
Format: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.
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.
23 of 24 people found the following review helpful
5.0 out of 5 stars
A great book for begginers.
17 May 1999
By saras@servidor.unam.mx
- Published on Amazon.com
Format: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.
24 of 26 people found the following review helpful
5.0 out of 5 stars
Perfect for New Grad Students
24 Nov 2002
By Owen Hehmeyer
- Published on Amazon.com
Format: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.
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4.3 out of 5 stars
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