Understanding Molecular Simulation (Computational Science Series, Vol 1)

  Author:    Daan Frenkel, B. Smit, Berend Smit
  ISBN:    0122673514
  Sales Rank:    175824
  Published:    2001-10-15
  Publisher:    Academic Press
  # Pages:    600
  Binding:    Hardcover
  Avg. Rating:    5.0 based on 8 reviews
  Used Offers:    8 from $65.70
  Amazon Price:    $66.36
  (Data above last updated:  2008-11-16 09:46:26 EST)
  
  
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Understanding Molecular Simulation (Computational Science Series, Vol 1)
  
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.
                  Reader Reviews 1 - 12 of 12                 
  
  
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02-08-08 4 0\1
(Hide Review...)  Understanding molecular simulation
Reviewer Permalink
This book is goof for studying molecular. For beginner, this book is easy to understand how to do.
(Review Data Last Updated: 2008-08-29 09:30:37 EST)
02-08-08 4 0\1
(Hide Review...)  Understanding molecular simulation
Reviewer Permalink
This book is goof for studying molecular. For beginner, this book is easy to understand how to do.
(Review Data Last Updated: 2008-11-16 09:48:26 EST)
05-07-07 5 (NA)
(Hide Review...)  great book for MD basics
Reviewer Permalink
I was especially delighted about the Monte Carlo methods and the free energy calculation techniques.
(Review Data Last Updated: 2008-02-15 14:33:49 EST)
11-10-06 3 (NA)
(Hide Review...)  A work of mediocrity
Reviewer Permalink
It covers many useful and practical tricks, which one may frequently need to look up. However the author has neither a clear mind nor enough intelligence to handle those topics from the top. And the book is by no means an inspiring one. In short, it's suitable for engineers, not for creative people.
(Review Data Last Updated: 2006-12-02 03:29:37 EST)
06-19-06 2 4\6
(Hide Review...)  Old fashioned fortran, strong bias on Monte Carlo
Reviewer Permalink
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.
(Review Data Last Updated: 2008-02-15 14:33:49 EST)
06-18-06 2 3\4
(Hide Review...)  Old fashioned fortran, strong bias on Monte Carlo
Reviewer Permalink
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.
(Review Data Last Updated: 2007-04-10 12:48:16 EST)
11-20-04 5 4\5
(Hide Review...)  Excellent text for beginners in simulation
Reviewer Permalink
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.
(Review Data Last Updated: 2008-02-15 14:33:49 EST)
11-19-04 5 3\3
(Hide Review...)  Excellent text for beginners in simulation
Reviewer Permalink
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.
(Review Data Last Updated: 2006-06-23 11:18:42 EST)
11-24-02 5 13\14
(Hide Review...)  Perfect for New Grad Students
Reviewer Permalink
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.

(Review Data Last Updated: 2008-02-15 14:33:49 EST)
08-30-01 4 24\26
(Hide Review...)  A nice disappointment
Reviewer Permalink
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.
(Review Data Last Updated: 2008-02-15 14:33:49 EST)
09-21-00 5 4\5
(Hide Review...)  An excellent introduction
Reviewer Permalink
This book is an excellent introduction to the field of molecular dynamics simulation. It is easy to follow for a scientist entering the field and at the same time contains overview of most critical topics in MD simulation. The book's major goal is to describe how to simulate liquids, however it also mentions briefly the methods for gas and liquid simulations. List of references for further readings is very useful and complete.
(Review Data Last Updated: 2007-12-14 02:45:29 EST)
05-17-99 5 18\18
(Hide Review...)  A great book for begginers.
Reviewer Permalink
This book covers many interesting topics in molecular simulation, both Monte Carlo and M.D. It focuses on understanding the main ideas rather than giving long codes. It's a good place to start, but it also covers some ideas not found in many other books. When I try to extend my molecular dynamics program I always check what Frenkel and Smit have to say about it.
(Review Data Last Updated: 2006-06-23 11:18:42 EST)
  
                  Reader Reviews 1 - 12 of 12                 
  
  
  
  
  
  

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