Chemical Education Today
The Art of Molecular Dynamics Simulation D. C. Rapaport. Cambridge University Press: New York, 1996. 400 pp. ISBN 0 521 44561 2. $74.95.
This book describes the extremely powerful techniques of molecular dynamics simulation. The techniques involve solving the classical many-body problems in contexts relevant to the study of matter at the atomic level. The method allows the prediction of static and dynamics properties of substances directly from the underlying interactions between molecules. This is, of course, a very broad subject and the author has adopted a dual approach in that the text is partly tutorial and also contains a large number of computer programs for practical use. Rapaport has adopted the attitude of trying the simplest method first. Atoms are modeled as point particles interacting through point potentials. Molecules are represented by atoms with orientation dependent forces, or as extended structures each containing several interaction sites. The molecules may be rigid, flexible, or somewhere in between, and if there are internal degrees of freedom there will be internal forces as well. The intent of the book is not to discuss the design of molecular models, but rather to make use of existing models, and from a pedagogical viewpoint the simpler the model the better. The aim of the book is to demonstrate the general methodology of molecular dynamics simulation by example, not to review the large body of literature covering the many different kinds of models developed for specific applications. The text is partly tutorial, but also contains a large number of computer programs for practical use. This volume will serve as an introduction to the subject for beginners and as a reference manual for the more experienced practitioner. The material covers a wide range of practical methods and real applications and is organized as a series of case studies. The typical case study includes a summary of the theoretical background used for the formulation of the computational approach. That is described by either a complete program listing or a series of modifications or additions to a program from an earlier case study. The initial conditions of the model, organization of the input and output, accuracy, convergence, and efficiency are also addressed for each case and, of course, the results of the computation are given and discussed.
The book begins with the simplest case of basic molecular dynamics, a sift-disk fluid. The development is discussed in considerable depth to set the tone of the work. Later chapters extend the basic model in various directions, deal with various types of measurements, improve the computational methods, and introduce new models for more complex problems. These chapters also discuss the methodology for simulating monatomic systems and focus on measuring the thermodynamic and structural properties of systems in equilibrium. Consideration is given to the dynamical properties of equilibrium systems, including transport coefficients and the correlation functions that characterize space- and time-dependent properties. Chapters are devoted to the study of systems under constant temperature and pressure and the dynamics of rigid systems. It is difficult to cover all aspects of such a broad topic as the subject of this book; and the author has not attempted an exhaustive or encyclopedic coverage, but has produced an excellent introduction to the subject. The publisher has made the implementation of the numerous programs essentially painless by making them available via browser and the World Wide Web. The easy availability of the software, written in C, was welcomed by this old Fortran programmer. It is to be hoped that this service is representative of a trend in technical publishing. Overall this work is a pleasure to read and study and would be a valuable addition to the library of both the beginner and the experienced practitioner of the art. Stephen P. Molner Foundation for Chemistry Upper Arlington, OH 43212-1112
JChemEd.chem.wisc.edu • Vol. 76 No. 2 February 1999 • Journal of Chemical Education
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