The Art of Molecular Dynamics Simulation
D. C. Rapaport

The software described here is intended to accompany the book The Art of Molecular Dynamics Simulation by D.C. Rapaport, published by Cambridge University Press (1995). The material is being supplied in computer-readable form to allow readers to follow the case studies in the book while avoiding the tedious (and error-prone) task of manually the inputting the text of the programs. More than 7000 lines of C code are included in the package that can be selectively compiled to produce a total of 43 different programs corresponding to the case studies described in the book. With only a little effort, a wide range of other MD simulations can be constructed from this material, including many of those suggested as Further Work at the end of each chapter.

The following are extracts from the Preface:

Molecular dynamics simulation provides the methodology for detailed microscopic modeling on the molecular scale. After all, the nature of matter is to be found in the structure and motion of its constituent building blocks, and the dynamics is contained in the solution to the N-body problem. Given that the classical N-body problem lacks a general analytical solution, the only path open is the numerical one. Scientists engaged in studying matter at this level require computational tools to allow them to follow the movement of individual molecules and it is this need that the molecular dynamics approach aims to fulfill.

This is a recipe book. More precisely, it is a combination of an introduction to MD for the beginner, and a cookbook and reference manual for the more experienced practitioner. The hope is that through the use of a series of case studies, in which real problems are studied, both goals can be achieved. The book can be read from cover to cover to explore the principles and capabilities of MD, or it can be used in cookbook style -- with a certain amount of cross-referencing -- to obtain the recipe for a particular kind of computation. Some familiarity with classical and statistical mechanics, numerical methods and computer programming is assumed.

The case studies take the reader through all the stages from initial problem statement to the presentation of the results of the calculation. The link between these endpoints is the computer program -- the recipe. The results of the simulations are experimental observations, in the sense that the simulation is an experiment conducted on an actual, albeit highly idealized, substance. Some of these observations amount to mere measurement, while others can include the discovery of qualitatively novel effects; the custom of referring to MD simulation as computer experimentation is most certainly justified.

http://www.cup.cam.ac.uk/onlinepubs/ArtMolecular/ArtMoleculartop.html

ftp://ftp.cup.cam.ac.uk/pub/science/ArtMolecular/artmdsim.tar.gz/

The author can be reached at the following e-mail address:
rapaport@bluegum.ph.biu.ac.il

Reports of bugs, as well as comments and suggestions, will be greatly appreciated.