Numerical Simulation in Molecular Dynamics: Numerics, Algorithms, Parallelization, Applications

✍ Scribed by Michael Griebel, Gerhard Zumbusch, Stephan Knapek (auth.)

• Publisher: Springer-Verlag Berlin Heidelberg
• Year: 2007
• Tongue: English
• Leaves: 472
• Series: Texts in Computational Science and Engineering 5
• Edition: 1
• Category: Library

✦ Synopsis

Particle models play an important role in many applications in physics, chemistry and biology. They can be studied on the computer with the help of molecular dynamics simulations. This book presents in detail both the necessary numerical methods and techniques (linked-cell method, SPME-method, tree codes, multipole technique) and the theoretical background and foundations. It illustrates the aspects modelling, discretization, algorithms and their parallel implementation with MPI on computer systems with distributed memory. Furthermore, detailed explanations are given to the different steps of numerical simulation, and code examples are provided. With the description of the algorithms and the presentation of the results of various simulations from the areas material science, nanotechnology, biochemistry and astrophysics, the reader of this book will be able to write his own programs for molecular dynamics step by step and to run successful experiments.

✦ Table of Contents

Front Matter....Pages I-XI
Computer Simulation — a Key Technology....Pages 1-15
From the Schrödinger Equation to Molecular Dynamics....Pages 17-36
The Linked Cell Method for Short-Range Potentials....Pages 37-111
Parallelization....Pages 113-150
Extensions to More Complex Potentials and Molecules....Pages 151-209
Time Integration Methods....Pages 211-237
Mesh-Based Methods for Long-Range Potentials....Pages 239-311
Tree Algorithms for Long-Range Potentials....Pages 313-389
Applications from Biochemistry and Biophysics....Pages 391-411
Prospects....Pages 413-416
Back Matter....Pages 417-470

✦ Subjects

Computational Science and Engineering; Numerical Analysis; Math. Applications in Chemistry; Mathematical and Computational Physics; Appl.Mathematics/Computational Methods of Engineering