Understanding Molecular Simulation (Computational Science Series, Vol 1)

Book Description

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.

Customer Reviews:

great book for MD basics.......2007-05-07

I was especially delighted about the Monte Carlo methods and the free energy calculation techniques.

Old fashioned fortran, strong bias on Monte Carlo.......2006-06-19

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 Allan/Tildesley, and many MD techniques which they consider "advanced" (such as cell list methods, verlet tables, etc.) are shifted to one of the many appendices. They do not talk about ghostparticles for instance or give a detailed account of parallelized algorithms which is really state-of-the art today.
The code examples for download for the exercises, contain subtle errors, are not optimized for performance (which is THE most important thing in simulation business) and worst of all, are written in Fortran. The fact that they publish Fortran code must reflect the fact that at the time they learned how to program a computer there was no C, C++, JAVA, etc. and no object orientation in sight. Nowadays, probably no expert in programming would start a scientific and readable code in fortran. Also their definition of an algorithm is simply technically wrong. The authors are very sloppy here, have obviously no training in theoretical computer science and are obviously no experts for writing optimal code.
Scientifically, as far as physics is concerned, the book is sound, they give good arguments pro and against certain methods, but when you have already worked with Allan/Tildesley or Rappaport for many years you have the eery impression that they simply repeat many arguments from these books or from other research articles (They keep citing Allan/Tildesley a lot) Those things that are not more or less copied from other sources seems to reflect their own experience in this field which seems to be strongly limited to MC methods.
Although this book is sometimes praised I cannot really recommend it. Allan/Tildesley, and in particular the book by Rappaport are superior in stlye and in particluar as code examples are concerned. With Rappaport you get working code right away in proper C (albeit in Fortran-Style C -- again, the reason for this being the fact, that all these authors of Simulation books learned programming probably in the late 70's when Fortran was state-of-the-art). I nevertheless would recommend Rappaports book instead. The authors even offer scientific workshops based on their book (and probably make a lot of money with that). One can only hope that those are better than the coding examples of the exercises. Therefore only 2 stars.

Excellent text for beginners in simulation.......2004-11-20

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.

Perfect for New Grad Students.......2002-11-24

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.

A nice disappointment.......2001-08-30

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.

Intermolecular and Surface Forces, Second Edition: With Applications to Colloidal and Biological Systems (Colloid Science)

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Great Service
A great text with lots of information in a small package.
Good book.
Fantastic Book
Forces you know or not????

Intermolecular and Surface Forces, Second Edition: With Applications to Colloidal and Biological Systems (Colloid Science)
Jacob N. Israelachvili
Manufacturer: Academic Press
ProductGroup: Book
Binding: Hardcover

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ASIN: 0123751810

Book Description

This book describes the roles of various intermolecular and interparticle forces in determining the properties of simple systems such as gases, liquids, and solids, of more complex colloidal, polymeric, and biological systems. The book provides a thorough grounding in theories and concepts of intermolecular forces, allowing students and researchers to recognize which forces are important in any particular system and how to control these forces.

Key Features
* Surface-force measurements
* Solvation and structural forces
* Hydration and hydophobic forces
* Ion-correlation forces
* Thermal fluctuation (steric and undulation) forces
* Particle and surface interactions in polymer melts and polymer solutions
* Contains worked examples, discussion topics, and more than 100 problems

Customer Reviews:

Great Service.......2007-10-08

The book was brand new and the shipping was fast.
Thank you for an easy transaction.

A great text with lots of information in a small package........2007-09-29

This text is perfect for the reader who can read graphs and diagrams. A picture is worth a thousand words and so are graphs and diagrams. This text is chock full of graphs with all the information that you may need for an undergraduate or graduate course. I love this book. Its an excellent reference.

Good book........2007-09-03

Was used for "intermolecular forces" class... Advanced, and I think, it could be useful for people who work with AFM.

Fantastic Book.......2005-07-23

If you want to learn about the title subject, this is a great intro book. And it's probably the most enjoyable theory book you are likely to own, if you purchase it.

Forces you know or not????.......2004-02-13

The above "reviewer" needs to learn the English language! What the hell is that guy trying to tell us? I'm glad the book is useful to the outdoors.

Book Description

The subject of this book — intermolecular interactions — is as important in physics as in chemistry and molecular biology. Intermolecular interactions are responsible for the existence of liquids and solids in nature. They determine the physical and chemical properties of gases, liquids, and crystals, the stability of chemical complexes and biological compounds.

In the first two chapters of this book, the detailed qualitative description of different types of intermolecular forces at large, intermediate and short-range distances is presented. For the first time in the monographic literature, the temperature dependence of the dispersion forces is discussed, and it is shown that at finite temperatures the famous Casimir-Polder asymptotic formula is correct only at narrow distance range. The author has aimed to make the presentation understandable to a broad scope of readers without oversimplification. In Chapter 3, the methods of quantitative calculation of the intermolecular interactions are discussed and modern achievements are presented. This chapter should be helpful for scientists performing computer calculations of many-electron systems.

The last two chapters are devoted to the many-body effects and model potentials. More than 50 model potentials exploited for processing experimental data and computer simulation in different fields of physics, chemistry and molecular biology are represented. The widely used global optimisation methods: simulated annealing, diffusion equation method, basin-hopping algorithm, and genetic algorithm are described in detail.

Book Description

Why does matter stick together? Why do gases condense to liquids, and liquids to solids? This book is a detailed historical account of how some of the leading scientists of the past three centuries have tried to answer these questions. Organized into four broad periods of advances in understanding, the first three are associated with Newton, Laplace and van der Waals, while the fourth gives an account of the successful use in the twentieth century of quantum and statistical mechanics to resolve most of the remaining problems.

Download Description

Why does matter stick together? Why do gases condense to liquids, and liquids to solids? This book provides a detailed historical account of how some of the leading scientists of the past three centuries have tried to answer these questions. The topic of cohesion and the study of intermolecular forces has been an important component of physical science research for hundreds of years. This book is organised into four broad periods of advances in our understanding. The first three are associated with Newton, Laplace and van der Waals. The final section gives an account of the successful use in the twentieth century of quantum mechanics and statistical mechanics to resolve most of the remaining problems. The book will be of primary interest to physical chemists and physicists, as well as historians of science interested in the historical origins of our modern day understanding of cohesion.

Customer Reviews:

A tale of why we stick together.......2005-08-05

This book provides the history of scientific thought into why things stick together. The book begins with a review of ancient Greek science, and the concept of atoms - objects too small to be divided. The text then picks up in the Enlightenment when scientists like Newton are pondering the question of how the physical world came about, and using experiments to guide their ideas. The major scientific discoveries and discoverers in the field of cohesion are detailed, including both theorists and experimentalists. These cover the fields of quantum mechanics, electrostatics, chemistry, and surface science. Basic principles are laid out such that any college student in science or engineering can understand the text. Overall, an insightful book, though not the most entertaining book to read.

Molecular Aggregation: Structure Analysis and Molecular Simulation of Crystals and Liquids (International Union of Crystallography Monographs on Crystallography)

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Molecular Aggregation: Structure Analysis and Molecular Simulation of Crystals and Liquids (International Union of Crystallography Monographs on Crystallography)
Angelo Gavezzotti
Manufacturer: Oxford University Press, USA
ProductGroup: Book
Binding: Hardcover

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Book Description

This book is divided in two parts. Part I provides a brief but accurate summary of all the basic ideas, theories, methods, and conspicuous results of structure analysis and molecular modelling of the condensed phases of organic compounds: quantum chemistry, the intermolecular potential, force
field and molecular dynamics methods, structural correlation, and thermodynamics. This Part is written in simple and intuitive form, so that the reader may easily find there the essential background for the discussions in the second part. Part II exposes the present status of studies in the
analysis, categorization, prediction and control, at a molecular level, of intermolecular interactions in liquids, solutions, mesophases, and crystals. The main focus is here on the links between energies, structures, and chemical or physical properties.

Intermolecular Forces (International Series of Monographs on Chemistry)

Average customer rating:

A lack of the cohesive force spells doom for Rigby et al

Intermolecular Forces (International Series of Monographs on Chemistry)
Geoffrey C. Maitland , and others
Manufacturer: Oxford University Press
ProductGroup: Book
Binding: Hardcover

Customer Reviews:

A lack of the cohesive force spells doom for Rigby et al.......1999-03-20

The obvious problems with the Parallax inversion effect was overlooked whilst writing this book leaving the section of hydrogen bonding rather sketchy and all in all a little vague. The author seemed to lack understanding of the subject matter and clearly needed to spend more time researching the base topics involved (esp. Hydrogen bonding anti-inversion relapse). I felt the book moved from one topic to the next with no real explanation of the autors thought processes (if any!). The book is slightly 'dated' in it's approach albeit an old book, but it was dated even in its day. The subject matter would have been far better served with a broader more flexible approach to the quantum - devience factors which seem out of reach of the reader. The book does have it's merits, Rigby clearly has his strengths in resolving the complex mathematical equations required to derive the Schrodinger Equation from first priciples. If this book was ever re-published (and prefferably proofed for errors (the last time it must have been done by a real layman)) it would be a great guide to all the forces between molecules. Alas so much potential squandered...misses greatness by a mile

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Chemical Physics of Free Molecules
Norman H. March , and J.F. Mucci
Manufacturer: Springer
ProductGroup: Book
Binding: Hardcover

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ASIN: 0306442701

Book Description

In this introductory chemical physics textbook, the authors discuss the interactions, bonding, electron density, and experimental techniques of free molecules, and apply spectroscopic methods to determine molecular parameters, dynamics, and chemical reactions.

Chemical Reactions in Organic and Inorganic Constrained Systems (NATO Science Series C:)

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Chemical Reactions in Organic and Inorganic Constrained Systems (NATO Science Series C:)

Manufacturer: Springer
ProductGroup: Book
Binding: Hardcover

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ASIN: 9027721750

Chemistry States of Matter and Intermolecular Forces Chapter 11 Resource File

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Chemistry States of Matter and Intermolecular Forces Chapter 11 Resource File

Manufacturer: Holt
ProductGroup: Book
Binding: Paperback
ASIN: 0030681367

Dielectrics Intermolecular Forces Optical Rotation (Documents on Modern Physics)

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Dielectrics Intermolecular Forces Optical Rotation (Documents on Modern Physics)

Manufacturer: Gordon & Breach Science Pub
ProductGroup: Book
Binding: Paperback

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ASIN: 0677004052

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