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Understanding Molecular Simulation: From Algorithms to Applications (Computational Science) [Hardcover]

Daan Frenkel , Berend Smit
4.5 out of 5 stars  See all reviews (2 customer reviews)
Price: 64.99 & FREE Delivery in the UK. Details
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Book Description

19 Oct 2001 Computational Science
"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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Product details

  • Hardcover: 664 pages
  • Publisher: Academic Press Inc; 2nd Revised edition edition (19 Oct 2001)
  • Language: English
  • ISBN-10: 0122673514
  • ISBN-13: 978-0122673511
  • Product Dimensions: 23.8 x 14.3 x 4 cm
  • Average Customer Review: 4.5 out of 5 stars  See all reviews (2 customer reviews)
  • Amazon Bestsellers Rank: 534,197 in Books (See Top 100 in Books)
  • See Complete Table of Contents

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Review

".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.

Inside This Book (Learn More)
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
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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
5.0 out of 5 stars A great book for begginers. 17 May 1999
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.
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4.0 out of 5 stars Great book 4 Feb 2014
Format:Hardcover|Verified Purchase
The code is in fortran, hence it is not so useful. It could be on c or c++ istead.
Τhe theory is well-organised and explained.
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Amazon.com: 4.4 out of 5 stars  14 reviews
37 of 41 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.
24 of 26 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 27 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.
8 of 11 people found the following review helpful
5.0 out of 5 stars Excellent text for beginners in simulation 19 Nov 2004
By Kanishk Rastogi - Published on Amazon.com
Format:Hardcover|Verified Purchase
Its an excellent book for those who are just beginners in MC & MD simulations. everything is very clearly explained with lot of examples and some related unsolved problems. the text explores this topic indetails with advanced chapters in later sections. Good for anybody int hsi field be it in materials science, physics or related fields.
5 of 8 people found the following review helpful
2.0 out of 5 stars Totally misses the mark, waste of time 8 Jun 2010
By Omega - Published on Amazon.com
Format:Hardcover|Verified Purchase
While the book is a legitimate effort to codify the study of molecular mechanics, etc...I found it to be obtuse and wholly frustrating. I often write programs to solve problems in chemistry and biology, and the underlying tenets that serve me well are ignored in this book. The book has a huge discussion about what other people have done to write Monte Carlo algorithms, for example. But they fail to emphasize the algorithmic nature of the computer program, instead aiming to teach graduate students how to reproduce code that other people have already written. Monte Carlo: works on everything, but good for little if you don't already know the answer.

A good program makes the right assumptions about the problem, and this book fails to communicate this essential balance at the core of molecular modeling: treatment of complexity vs. exhaustiveness of sampling. There is a huge discussion of thermostats, etc. It is like trying to have a friendly debate with a friend who can't let go of the details to agree that the whole discussion is focused on the wrong topic. We write programs to solve problems algorithmically....the focus should be the algorithms, not the programs.

Unfortunately, I can't recommend a good alternative textbook. Rather, there is a wealth of information in journal articles and in the source code of several excellent open source projects. A reader/student would be well-served to identify those articles/projects that are personally most interesting, and study these rather than read this textbook.
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