The Art of Molecular Dynamics Simulation [Paperback]

D. C. Rapaport (Author)

Book Description

ISBN-10: 0521599423 | ISBN-13: 978-0521599429 | Publication Date: April 28, 1997 | Edition: 1

This book describes the extremely powerful technique of molecular dynamics simulation, which involves solving the classical many-body problem in contexts relevant to the study of matter at the atomic level. The method allows the prediction of the static and dynamic properties of substances directly from the underlying interactions between the molecules. Because there is no alternative approach capable of handling such a broad range of problems at the required level of detail, molecular dynamics methods have proved themselves indispensable in both pure and applied research. This volume will be of value to advanced students and researchers in physics, chemistry, polymer science and materials science in universities and industrial laboratories.

Editorial Reviews

Review

'The book is very thorough ... wide-ranging, clearly written and easy to follow ... All in all a most useful book. I recommend it strongly to all researchers involved with molecular dynamics.' M. G. B. Drew, Computers and Chemistry

'What Press et al.'s Numerical Recipes ... did for scientific computing in general, Dennis Rapaport's new book will do for the field of molecular-dynamics ... simulation ... Rapaport's book is useful ... and it deserves wide readership.' R. L. Blumberg Selinger, Computers in Physics

'The book itself is well written and deals easily with the complexities of the subject. I would gladly recommend it to any researcher in the field.' Chemistry & Industry

Book Description

This book describes the extremely powerful technique of molecular dynamics simulation, which involves solving the classical many-body problem in contexts relevant to the study of matter at the atomic level. The method allows the prediction of the static and dynamic properties of substances directly from the underlying interactions between the molecules.

Product Details

• Paperback: 414 pages
• Publisher: Cambridge University Press; 1 edition (April 28, 1997)
• Language: English
• ISBN-10: 0521599423
• ISBN-13: 978-0521599429
• Product Dimensions: 9 x 6.1 x 0.8 inches
• Shipping Weight: 1.2 pounds
• Average Customer Review: 3.7 out of 5 stars  See all reviews (9 customer reviews)
• Amazon Best Sellers Rank: #2,943,794 in Books (See Top 100 in Books)

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Customer Reviews

Most Helpful Customer Reviews

15 of 15 people found the following review helpful:

4.0 out of 5 stars Useful, for the right reader, May 9, 2005

By 

wiredweird "wiredweird" (Earth, or somewhere nearby) - See all my reviews
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This review is from: The Art of Molecular Dynamics Simulation (Paperback)

I'm not sure I'm that reader.

The ideal reader is wholly at home with good bits of analysis - you'll be comfortable with Lagrange multipliers, LU decomposition, quaternion representation of oriented values, and a fair bit else. You won't need the basics of classical physics, including Hamiltonians and a few projections of the Navier-Stokes equations down into tractable form. Non- and in-equilibrium dynamics, smooth and discrete representations, plus their mixed forms - you're prepared to build up from these elements.

You, the ideal reader, are not much of a programmer, though. The book built very much around extensive C sample code. I use the term "C" in some strict syntactic sense, though. The general style reminds me of FORTRAN, but the global data declarations are in the style of pre-1980 BASIC. This book is aimed at the odd mix of capable numerical analyst (which I'm not) and chemist (which I'm not), but naive software developer (which I'm not).

The strength of this book is in its code samples. The author explictly invites modification and extension. The only sane way to modify this code is to understand it thoroughly, and to understand the underlying chemistry, physics, and numerical models.

Maybe this book works well for some people, people that I admire immensely. I just wish it worked better for me.

//wiredweird

17 of 18 people found the following review helpful:

5.0 out of 5 stars Excellent introduction to MD simulation, March 24, 2000

By 

Alan Mason - See all my reviews

This review is from: The Art of Molecular Dynamics Simulation (Hardcover)

Strengths: Excellent selection of topics, with good references and enough discussion of the underlying scientific theory. Thoughtful and well-written. DO NOT USE MERELY AS A COOKBOOK!

Weaknesses: Antiquated code, basically FORTRAN with a C veneer. Although the code works as is and is blazingly fast, it's not usable as a basis for further code development -- readers will want to recast the ideas and algorithms in their own up-to-date C code. For example, his arrays start at 1; the only data structure is the array (ugh!), there are no structures. Things get hard to understand when he starts packing multiple array indices into a single composite index, then unpacks it (see, e.g., the code on autocorrelation functions, Chap. 5).

However, the awkward code is a blessing in disguise -- write your own and you'll learn an incredible amount! This book gives you all the conceptual tools to do this, and you can use the code supplied (available from the publisher) as a benchmark and check. Actually, there are a few bugs in the code, but considering its complexity (much of which is unavoidable), it is remarkably reliable. In general, the code is optimized for efficiency, not for ease of maintenance or generalization.

The author deserves any amount of thanks for writing this unique and indispensable book, which is clearly the fruit of many years of practical computing experience in a 70's, early 80's UNIX environment. The code has not aged well, but the ideas it embodies are timeless.

9 of 9 people found the following review helpful:

2.0 out of 5 stars Too much and too little., May 29, 2002

By 

Britt Park "brittpark" (Scotts Valley, CA United States) - See all my reviews
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This review is from: The Art of Molecular Dynamics Simulation (Paperback)

This book is in some ways a reasonable introduction to MD. It's the only book I know that actually shows the derivatives of energy functions necessary for writing efficient MD code. Unfortunately it does so in a hard to follow way. This is typical of the rest of the text. The example C code is hideous both in format and style. Missing from the book are essential formulae for calculating macroscopic properties from MD simulations. It is probably the best practical guide to writing MD code, but that isn't saying much.