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The Art of Molecular Dynamics Simulation [Kindle Edition]

D. C. Rapaport
4.5 out of 5 stars  See all reviews (2 customer reviews)

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Book Description

The extremely powerful technique of molecular dynamics simulation involves solving the classical many-body problem in contexts relevant to the study of matter at the atomistic level. Since there is no alternative approach capable of handling this extremely broad range of problems at the required level of detail, molecular dynamics methods have proved themselves indispensable in both pure and applied research. This book, first published in 2004, is a blend of tutorial and recipe collection, providing both an introduction to the subject for beginners and a reference manual for the more experienced practitioner. It is organized as a series of case studies that take the reader through each of the steps from formulating the problem, developing the necessary software, and then using the programs to make actual measurements. The second edition of the book includes a substantial amount of new material as well as completely rewritten software.

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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

  • Format: Kindle Edition
  • File Size: 94817 KB
  • Print Length: 564 pages
  • Simultaneous Device Usage: Up to 4 simultaneous devices, per publisher limits
  • Publisher: Cambridge University Press; 2 edition (1 April 2004)
  • Sold by: Amazon Media EU S.à r.l.
  • Language: English
  • ASIN: B00AKE1QUY
  • Text-to-Speech: Enabled
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  • Word Wise: Not Enabled
  • Enhanced Typesetting: Not Enabled
  • Average Customer Review: 4.5 out of 5 stars  See all reviews (2 customer reviews)
  • Amazon Bestsellers Rank: #1,704,330 Paid in Kindle Store (See Top 100 Paid in Kindle Store)

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5.0 out of 5 stars A great book, with lots of useful code in C 17 May 1999
By A Customer
Format:Hardcover
This is a great book on molecular dynamics. It covers lot's of interesing topics. Unfortunately most of the info is not explicitly written, but hidden in the included code. If you already know how to program in C and take the time to examine and analyize the programs you can get some really good code.
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By A Customer
Format:Hardcover
This is a recipe book. More precisely, it is a combination of an introduction

to MD for the beginner, and a cookbook and reference manual for the more

experienced practitioner. Further information can be found at:

[...]
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Most Helpful Customer Reviews on Amazon.com (beta) (May include reviews from Early Reviewer Rewards Program)
Amazon.com: 3.9 out of 5 stars  11 reviews
16 of 18 people found the following review helpful
4.0 out of 5 stars Useful, for the right reader 10 May 2005
By wiredweird - Published on Amazon.com
Format:Paperback|Verified Purchase
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
0 of 1 people found the following review helpful
5.0 out of 5 stars Five Stars 24 Oct. 2014
By RadLab - Published on Amazon.com
Format:Hardcover|Verified Purchase
Exactly as described; quick delivery!
20 of 21 people found the following review helpful
5.0 out of 5 stars Excellent introduction to MD simulation 24 Mar. 2000
By Alan Mason - Published on Amazon.com
Format: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.
5 of 6 people found the following review helpful
4.0 out of 5 stars A good introduction to Molecular Dynamics 30 Aug. 2001
By Jose R. Valverde Carrillo - Published on Amazon.com
Format:Paperback
This book constitutes a good introduction to the methods of Molecular Dynamics. Besides clear descriptions of the methods and algorithms, it includes C example implementations commented on the book to illustrate the points. It is almost an introducory 'recipe' book. For advanced tips, Frenkel-Smit will give good lead, but at the cost of less readability and Fortran (pseudo)code.
Certainly, the underlying philosophy of the code may seem awkward initially, but it is not a matter of "C design", rather of coding philosophy and program design. Once you get to understand it, it becomes easy and "natural". And what's even more important: it reflects the program design philosophy in use in the Molecular Modelling field, hence getting used to it will help you understand most existing production code.
The electronic version of the C code (available at the book's web site) is a mesh though: it lacks comments and makes heavy use of conditional compilation to render the examples from a single, convoluted source. The ingenious programmer won't be misled by this however: a simple step with the C preprocessor will distil the actual code. Not to mean it is not inconvenient anyway (sic). Certainly, it would have been a lot better if the authors had separated, cleaned and commented the code for the examples in the electronic version.
Besides, the book comes with additional, not too difficult programming assignments that make for extra fun and deeper understanding.
Once you are done with this book, you'll be in a position to really appreciate and use Frenkel-Smit and other advanced texts.
4 of 4 people found the following review helpful
3.0 out of 5 stars Not really C 16 Aug. 1999
By jonnyl@iname.com - Published on Amazon.com
Format:Paperback
The code examples are in C, but the author tries to write it "Fortran style". Basically it seems almost as if the code was converted from Fortran code to C by f2c (a GNU translation program). It really seems as if the author's background is in Fortran and hasn't really grasped the fundamental C approach to writing code. However, if you can manage to decipher the code, the technical information is very useful. Most molecular dynamics books still seem to be directed at the Fortran audience, so this is probably as close as you will come to a book for the C audience.
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