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Molecular dynamics simulation
journal of I~IOLECULAR
LIQUIDS ELSEVIER
Journal of Molecular Liquids 75 (1998) 271-272
Book
Review
J.M.Haile: Molecular Dynamics S i m u l a t i o n . Wiley Professional Paperback Edition, Wiley & Sons, Inc., New York, 1997. ISBN 0-471-18439-X
This book appeared first in 1992. It is now (1997) available in the ' Wiley Professional Paperback Series'. The author states in the prologue in Chapter 1 that the book is an introduction to the methodology of molecular dynamics (MD) for the newcomer. Only little information is given on the multitude of applications of this widely spread method. The objective is the presentation of fundamentals that should be commonly known. Molecular dynamics requires knowledge on several disciplines, such as mechanics, statistical mechanics, and thermodynamics, on vector calculus and numerial methods as well as on Fortran programming. As an important part of computer simulation methods it has become an respected research tool, complementing the traditional approaches of theory and experiment. MD differently to the Monte Carlo (MC) method permits the study of nonlinear dynamical behavior of many-body-systems. Predictability and determinism of such calculations are central for the methodology. In the authors mind it is the deterministic unpredictability which makes MD so fascinating and challenging. Molecular simulations are theoretical tools with models primarily independent of measurements on real systems. A model consists in giving the interaction laws between the parts inside the system and the interaction laws between the particles and the surroundings. No attempt is made in the book to describe the development of models. Very simple model potentials such as hard.spheres and Lennard-Jones potentials are used to explain the features of simulation. The validity of a simulation is discussed in some detail. Very rarely there are possibilities, to test it with the help of known results from an analytic theory. More often it results from an analysis of the accumulation of possible simulation errorrs and arguing, that their effect lies within the tolerance for a given simulation. Chapter 2 deals with fundamentals such as the classification of dynamical systems, integrability and ergodicity, as well as with the determination of properties, elements of sampling theory and periodic boundary conditions. The description of systems of hard bodies in terms of elastic collisions is somewhat simpler and not as time consuming as the full solution of the equations of motion for continuous potentials, b:inematics of hard sphere collisions is therefore treated in Chapter 3 together with a characterization of an order - disorder transition, called melting transition. Chapter 4 informs the reader about the solution by finite difference methods of initial value problems of systems of ordinary differential equations. Different algorithms - the 0167-7322/98/$19.00 © 1998 Elsevier Science B.V. All rights reserved 00106-2
Pll SO 167-7322(97)
272 heart of each MD program - are compared. Tests of the reliability of the computed trajectories are executed by the comparison of the results of different simulations with theoretical equilibrium properties of a one-dimensional soft-sphere system. In Chapter 5 a proper treatment of model interaction potential functions is analyzed. Potential truncation, shifted-force, minimum-image and other conventions such as neighbor lists are introduced and discussed. Chapter 6 shows how to obtain static properties from a simulation run, e.g., various thermodynamic functions and structural quantities such as pair correlation functions. The achievment of dynamic properties as time correlation functions and transport coefficients from MD simulations is discussed in Chapter 7. All together the book provides a valuable introduction to the methodology of molecular dynamical simulation of classical dense systems. The relevant literature is referenced for every chapter. Especially useful are exercises at the end of each chapter, deepening its content. The example programs collected in different appendices can be easily transported to a computer. They are well selected to give the reader an impression how a simple MD program works. As an introductory text to MD this book can be warmly recommended to beginners, who are interested in this field and want to understand the underlying principles of MD. Hartmut Krienke, Regensburg
LIQUIDS ELSEVIER
Journal of Molecular Liquids 75 (1998) 271-272
Book
Review
J.M.Haile: Molecular Dynamics S i m u l a t i o n . Wiley Professional Paperback Edition, Wiley & Sons, Inc., New York, 1997. ISBN 0-471-18439-X
This book appeared first in 1992. It is now (1997) available in the ' Wiley Professional Paperback Series'. The author states in the prologue in Chapter 1 that the book is an introduction to the methodology of molecular dynamics (MD) for the newcomer. Only little information is given on the multitude of applications of this widely spread method. The objective is the presentation of fundamentals that should be commonly known. Molecular dynamics requires knowledge on several disciplines, such as mechanics, statistical mechanics, and thermodynamics, on vector calculus and numerial methods as well as on Fortran programming. As an important part of computer simulation methods it has become an respected research tool, complementing the traditional approaches of theory and experiment. MD differently to the Monte Carlo (MC) method permits the study of nonlinear dynamical behavior of many-body-systems. Predictability and determinism of such calculations are central for the methodology. In the authors mind it is the deterministic unpredictability which makes MD so fascinating and challenging. Molecular simulations are theoretical tools with models primarily independent of measurements on real systems. A model consists in giving the interaction laws between the parts inside the system and the interaction laws between the particles and the surroundings. No attempt is made in the book to describe the development of models. Very simple model potentials such as hard.spheres and Lennard-Jones potentials are used to explain the features of simulation. The validity of a simulation is discussed in some detail. Very rarely there are possibilities, to test it with the help of known results from an analytic theory. More often it results from an analysis of the accumulation of possible simulation errorrs and arguing, that their effect lies within the tolerance for a given simulation. Chapter 2 deals with fundamentals such as the classification of dynamical systems, integrability and ergodicity, as well as with the determination of properties, elements of sampling theory and periodic boundary conditions. The description of systems of hard bodies in terms of elastic collisions is somewhat simpler and not as time consuming as the full solution of the equations of motion for continuous potentials, b:inematics of hard sphere collisions is therefore treated in Chapter 3 together with a characterization of an order - disorder transition, called melting transition. Chapter 4 informs the reader about the solution by finite difference methods of initial value problems of systems of ordinary differential equations. Different algorithms - the 0167-7322/98/$19.00 © 1998 Elsevier Science B.V. All rights reserved 00106-2
Pll SO 167-7322(97)
272 heart of each MD program - are compared. Tests of the reliability of the computed trajectories are executed by the comparison of the results of different simulations with theoretical equilibrium properties of a one-dimensional soft-sphere system. In Chapter 5 a proper treatment of model interaction potential functions is analyzed. Potential truncation, shifted-force, minimum-image and other conventions such as neighbor lists are introduced and discussed. Chapter 6 shows how to obtain static properties from a simulation run, e.g., various thermodynamic functions and structural quantities such as pair correlation functions. The achievment of dynamic properties as time correlation functions and transport coefficients from MD simulations is discussed in Chapter 7. All together the book provides a valuable introduction to the methodology of molecular dynamical simulation of classical dense systems. The relevant literature is referenced for every chapter. Especially useful are exercises at the end of each chapter, deepening its content. The example programs collected in different appendices can be easily transported to a computer. They are well selected to give the reader an impression how a simple MD program works. As an introductory text to MD this book can be warmly recommended to beginners, who are interested in this field and want to understand the underlying principles of MD. Hartmut Krienke, Regensburg