The Art of Molecular Dynamics Simulation

Book 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 software. First Edition Hb (1996): 0-521-44561-2 First Edition Pb (1996): 0-521-59942-3

Customer Reviews:

Useful, for the right reader.......2005-05-10

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

Too much and too little........2002-05-30

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.

A good introduction to Molecular Dynamics.......2001-08-30

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.

Good book on subject, needs a REAL C second edition.......2000-08-05

This is a good and honest book on the subject, it needs a second edition in pure C language and not the 'f2c-like' used. Many techiques like linked lists are simple and clear in C but confuse when translated to Fortran (77 or the new 90/95 variants)

Excellent introduction to MD simulation.......2000-03-25

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.

Book Description

This book is concerned with a wide range of general principles that govern the behaviour of atoms in solids, and these principles are applied to the full range of types of materials known to man. The dual focus is on the structures of materials at an atomic level and on how the atoms vibrate inside solids. This dual focus comes together to explore how the atomic principles determine the behaviour and properties of materials. Attention is also given to experimental methods. The general principles include the factors that determine the packing of atoms to form the huge variety of structures, the formal description of real and reciprocal space, the types of atomic bonding, the formalism of atomic vibrations, and the theories of phase transitions. The tools covered include diffraction and spectroscopy, both laboratory and large-scale facilities.

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Atomic Dynamics in Liquids
N. H. March , and M. P. Tosi
Manufacturer: Dover Publications
ProductGroup: Book
Binding: Paperback

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Introduction to Liquid State Physics

ASIN: 0486665984

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This distinguished work by two leading authorities in the field covers static structure and thermodynamics; calculation of liquid structure from a law of force; liquid dynamics and time-dependent correlation functions; hydrodynamic forms of correlation functions and generalized hydrodynamics; microscopic theories of the van Hove function; and other topics. 1976 edition.

Applications of Synchrotron Radiation: High-Resolution Studies of Molecules and Molecular Adsorbates on Surfaces (Lecture Notes in Computer Science)

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Charge and Energy Transfer Dynamics in Molecular Systems: A Theoretical Introduction

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Providing a unified description of different transfer phenomena in molecular systems, this volume serves as an introduction for graduate students and researchers. The authors manage to bridge the regimes of coherent and dissipative dynamics and thus establish the connection between classic rate theories and modern treatments of ultrafast phenomena.
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Dynamical Properties of Solids
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Manufacturer: Elsevier Science Ltd
ProductGroup: Book
Binding: Hardcover

Book Description

The first two volumes in this series published twenty years ago contained chapters devoted to anharmonic properties of solids, ab initio calculations of phonons in metals and insulators, and surface phonons. In the intervening years each of these important areas of lattice dynamics has undergone significant developments. This volume is therefore concerned with reviewing the current status of these areas.

Chapter one deals with the path-integral quantum Monte-Carlo method as a numerical simulation approach and looks at how this has been applied successfully to the determination of low temperature thermodynamic properties of anharmonic crystals and to certain dynamical properties as well. Chapter two is concerned with the calculation of static and dynamic properties of anharmonic crystals in the quantum regime. Chapter three discusses intrinsic anharmonic localized modes that have been intensively studied recently. Two topics, ab initio calculations of phonons in metals, and surface phonons are dealt with in the next chapter. The remaining two chapters are devoted to topics that have not been treated in previous volumes. One is phonon transport and the second is phonons in disordered crystals.

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Knowledge of the dynamics of many-electron systems is of fundamental importance to all disciplines of condensed matter physics. A very effective access to electron dynamics is offered by inelastic X-ray scattering (IXS) spectroscopy. The double differential scattering cross section for IXS is directly related to the time-dependent two-particle density correlation function, and, for large momentum and energy transfer (Compton limit) to the electron momentum distribution. Moreover, resonant inelastic X-ray scattering (RIXS) enables the study of electron dynamics via electronic excitations in a very selective manner (e.g. selectively spin, crystal momentum, or symmetry), so that other methods are efficaciously complemented. The progress of IXS spectroscopy is intimately related to the growing range of applications of synchrotron radiation. The aim of the book is to provide the growing community of researchers with accounts of experimental methods, instrumentation, and data analysis of IXS, with representative examples of successful applications, and with the theoretical framework for interpretations of the measurements.

Helium Cryogenics (International Cryogenics Monograph Series)

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useful book

Helium Cryogenics (International Cryogenics Monograph Series)
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useful book.......2000-05-31

It is an useful book for an engineer of cyrogenics.

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This volume details the application of molecular simulation to the liquid state. It is organised in a clear and logical way that first takes the reader through the underlying statistical mechanical theory necessary to understand the liquid state, especially those aspects that can be taken advantage of by simulation to help unravel the nature of the liquid state. It continues by covering the various modern variants of the Monte Carlo and Molecular dynamics techniques, for example, Gibbs ensemble MC and alternative ensemble MD. The effects of molecular architecture and chemical composition on the microscopic and macroscopic behaviour of liquids are also covered. The author has included chapters on surfaces, equations of state and phase equilibria, which emphasise new simulation techniques and conclusions made from the theories. Langmuir films, liquid crystals and the glassy state are also considered.

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General | Physics | Science | Subjects | Books

Book Description

The possibilities of molecular dynamcis (MD) simulations have recently been greatly extended by the development of new methods and by rapid advances in computers. DM simulations show great potential in condensed matter physics, where their success is not confined to numerical aspects of detailed analysis of physical systems; MD simulations have not verified same unexpected facts and introduced concepts that had been predicted previously from analytical theories. Molecular Dynamics Simulations details the current status of this field and investigates possible ways of increasing the efficiency of the silmulations and broadening the range of applicability of molecular dynamics techniques. The contributions, which are all written by leading researchers who have played major roles in developing the new simulation methods appearing in the last few years, range from background reviews to reports of recent research on supercooled liquid and glass transitions, oxides and multi-component materials fluids, and ab initio molecular dynamics simulations.

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Somewhat predictable, but a fun read

Complete Fun!

Flat and Disappointing

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Your Big Break
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ASIN: 0425207846

Book Description

Dani Myers has become an expert at romantic breakups ever since she was hired to "facilitate" them for clients of Your Big Break, Inc. In other words, she dumps people for money. But company rule #5 (do not get personally involved) is getting harder to obey. One of her dumpees is turning out to be the kind of guy she might just want to pick up on the rebound. and a new client has just walked in, begging for Dani's help breaking up with The Big Jackass, who's been leading her on all this time-and now turns out to be married.

It would be a routine job except for one problem: the so-called Big Jackass is married to none other than Dani's mother.

Customer Reviews:

Somewhat predictable, but a fun read.......2007-07-14

I have to say, I enjoyed reading this book. I like the way Johanna Edwards writes, and I love the fact that her heroines are not stick thin bleach blonde barbies (not that there's anything wrong with that, but you just get tire of the same gir being portrayed over and over again).
About half way through you could kind of figure out how the story would end, but that didn't take away from the experience of the book.
I'd definitely recommend this book and author to my friends.

Complete Fun!.......2007-02-26

Dani Myers is a "communication specialist." English translation: Dani breaks up with people for a living. She'll even quit your job for you. Dani loves what she does until the unthinkable happens. She receives a new client that wants to hire her to break up with Dani's own father. If that isn't bad enough, her parents are still married.

Dani is thrown for a loop. Should she tell her mother? Should she break up with her own father? Dani must figure it out or risk losing her job!

This book was so cute and so much fun! This was my first encounter with Johanna Edwards and I really enjoyed her work. Her writing style was light and funny. The plot was unique and interesting. I would definitely recommend this novel to someone who is looking for a unique take on chick lit.

I give this novel 4 out of 5 stars.

Flat and Disappointing.......2006-08-26

I read and enjoyed the author's first book and looked forward to this one. I tried to like it, but was disappointed. The plot concept seemed original, but the book itself just seemed flat, no pun intended, and devoid of any real charm. The characters weren't particularly appealing and though I finished the book, it was a bit of a struggle. But, hey, maybe it's me :) Sometimes when you have high expectations, you're set up for a let-down. Wish I could recommend this book, but I just didn't enjoy it as much as I'd expected.

liked it better than the first book.......2006-06-09

I actually liked this book better than The Next Big Thing. It was so much fun and truly original. I laughed the whole way through and the book was an extremely quick read. I picked it up for vacation and finished it in three days. Definitely recommended. My only critique is the ending came a little too fast. But overall this is a winner!

Just Not Getting It........2006-06-08

After reading the reviews here, I feel like I am losing my sense of humor. Everyone seems to laud this book as "hysterical", but I didn't get that sense at all. The storyline was predictable, the characters lacked depth, and the dialogue was forced. I really liked her first book a lot, but I have to say that I just don't recommend this one.

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Title: Break on through: remove barriers to your big dreams by following these simple steps.(BE YOUR OWN BOSS: SUCCESS COACH)(Business Success)
Author: Romanus Wolter
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From the supplier: Opportunities for African Americans in the field of creative arts remain scarce. Given this environment, black hopefuls should find alternative ways of getting a foot in the door. In film and television, individuals should either find any job that will give them contact with other industry people or create a sample of their work. Individuals who are interested in theater, on the other hand, have to develop their own work and income opportunities. A career in dance can be advanced by working in a university while visual artists can do work in the advertising and publishing world. Fortunately, the music sector is relatively easier to penetrate.

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