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

by Michael Griebel, Stephan Knapek, Gerhard Zumbusch

This book details the necessary numerical methods, the theoretical background and foundations and the techniques involved in creating computer particle models, including linked-cell method, SPME-method, tree codes, amd multipol technique. It illustrates modeling, discretization, algorithms and their parallel implementation with MPI on computer systems with distributed memory. The text offers step-by-step explanations of numerical simulation, providing illustrative code examples. With the description of the algorithms and the presentation of the results of various simulations from fields such as material science, nanotechnology, biochemistry and astrophysics, the reader of this book will learn how to write programs capable of running successful experiments for molecular dynamics.

488 pages, Paperback

First published August 9, 2007

Reviews

[Nikola Tchipev · Rating 4 out of 5]

Overall a good book, but one thing, which is missing is a thorough discussion of Verlet Neighbourhood lists. If you just read the book, you get the impression that the Linked Cell Method is the way to go. But nowadays it isn't - most of the bigger MD packages use Verlet Neighbourhood lists, as they can be much faster than Linked Cells for certain simulation parameters (single-centered Lennard-Jones atoms - up to Factor 2-3). For other simulation parameters they are relatively equal in performance, so the fact that they can be up to factor 3 faster in some cases tilts the decision in favour of Neighbourhood lists.
Also, the treatment on the Fast Multipole Method is incomplete.

[Martina · Rating 4 out of 5]

Despite not reading this book in its entirety, I can tell that it's very good. True, I've just skimmed through the first chapters, but just because I'm somewhat acquainted with molecular dynamics and don't need to brush up on things that I have learned/read about recently. For a person initiated in MD, reading the book won't pose any kind of problem, since it reads nicely if you already know a thing or two about MD. However, the select chapters I have read were informative and interesting. I especially liked the chapter on applications, which has helped me in troubleshooting my own project. If we omit the fact that not everyone of us has a cluster on which he/she can run simulations, the book is quite relatable ;)