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

Daan Frenkel , Berend Smit
4.4 out of 5 stars  See all reviews (14 customer reviews)

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Book Description

November 7, 2001 0122673514 978-0122673511 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.

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Understanding Molecular Simulation, Second Edition: From Algorithms to Applications (Computational Science) + Computer Simulation of Liquids + Molecular Modelling: Principles and Applications (2nd Edition)
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Editorial Reviews

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 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.

Product Details

  • Series: Computational Science
  • Hardcover: 664 pages
  • Publisher: Academic Press; 2 edition (November 7, 2001)
  • Language: English
  • ISBN-10: 0122673514
  • ISBN-13: 978-0122673511
  • Product Dimensions: 1.6 x 5.6 x 9.2 inches
  • Shipping Weight: 2.2 pounds (View shipping rates and policies)
  • Average Customer Review: 4.4 out of 5 stars  See all reviews (14 customer reviews)
  • Amazon Best Sellers Rank: #148,838 in Books (See Top 100 in Books)

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Customer Reviews

Most Helpful Customer Reviews
37 of 41 people found the following review helpful
4.0 out of 5 stars A nice disappointment August 30, 2001
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.
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24 of 26 people found the following review helpful
5.0 out of 5 stars A great book for begginers. May 16, 1999
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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24 of 27 people found the following review helpful
5.0 out of 5 stars Perfect for New Grad Students November 23, 2002
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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8 of 11 people found the following review helpful
5.0 out of 5 stars Excellent text for beginners in simulation November 19, 2004
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.
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1 of 2 people found the following review helpful
5.0 out of 5 stars classical on molecular simulation May 25, 2010
Format:Hardcover|Verified Purchase
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.
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4 of 7 people found the following review helpful
5.0 out of 5 stars An excellent introduction September 21, 2000
Format:Hardcover
This book is an excellent introduction to the field of molecular dynamics simulation. It is easy to follow for a scientist entering the field and at the same time contains overview of most critical topics in MD simulation. The book's major goal is to describe how to simulate liquids, however it also mentions briefly the methods for gas and liquid simulations. List of references for further readings is very useful and complete.
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0 of 1 people found the following review helpful
5.0 out of 5 stars It's a good book December 29, 2013
Format:Hardcover|Verified Purchase
First it looks good, and then apparently it's new and in good quality with every page. I will read it and use it carefully, cos I want keep for very long time.
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Most Recent Customer Reviews
4.0 out of 5 stars Great book to begin with
This is a very didactic book, covering the basics aspects of molecular simulations methods (both MC and MD) in a relatively easy fashion.
Published 9 months ago by Peter
2.0 out of 5 stars Totally misses the mark, waste of time
While the book is a legitimate effort to codify the study of molecular mechanics, etc...I found it to be obtuse and wholly frustrating. Read more
Published on June 8, 2010 by Omega
5.0 out of 5 stars Excellent
Got a new book for real cheap. Delivered timely and the packaging was really good. I would recommend this book to anyone beginning with Molecular Simulations or Modeling.
Published on February 22, 2010 by Yogendra Pandey
5.0 out of 5 stars Good deal
This book is brand new and of high quality. What's more, the price is pretty good. Thanks for the customer service.
Published on November 25, 2008 by Howie
4.0 out of 5 stars Understanding molecular simulation
This book is goof for studying molecular. For beginner, this book is easy to understand how to do.
Published on February 8, 2008 by Kiyofumi Kurumisawa
5.0 out of 5 stars great book for MD basics
I was especially delighted about the Monte Carlo methods and the free energy calculation techniques.
Published on May 6, 2007 by Lorant Janosi
2.0 out of 5 stars Totally Old fashioned fortran, dissapointing
There is a very strong bias to MC methods in the book. What they have to say about Molecular Dynamics methods is not really new, most of it is virtually copied from the classic by... Read more
Published on June 18, 2006 by A. Einstein
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