- ISBN13: 9780521825689
- Condition: NEW
- Notes: Brand New from Publisher. No Remainder Mark.
Product Description
In this Second Edition an extensive series of detailed case studies introduces the reader to solutions to a variety of problems connected with the way molecular interactions and motions determine the properties of matter. The methods are widely used in studying phenomena involving everything from the simplest of liquids to highly complex molecules such as proteins. In addition to a significant amount of new material, this edition features completely rewritten softwa… More >>
The Art of Molecular Dynamics Simulation
Tags: case studies, liquids, molecular dynamics simulation, molecular interactions, molecules, motions, phenomena, properties of matter, proteins
#1 by Alan Mason on June 28, 2010 - 7:28 am
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.
Rating: 5 / 5
#2 by wiredweird on June 28, 2010 - 8:53 am
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
Rating: 4 / 5
#3 by Britt Park on June 28, 2010 - 11:34 am
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.
Rating: 2 / 5
#4 by jonnyl@iname.com on June 28, 2010 - 12:47 pm
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.
Rating: 3 / 5
#5 by Anonymous on June 28, 2010 - 3:43 pm
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:
http://www.cup.cam.ac.uk/onlinepubs/artmolecular/ArtMoleculartop.html
Rating: 4 / 5