Numerical simulation in molecular dynamics. Numerics, algorithms, parallelization, applications. (English) Zbl 1131.76001
Texts in Computational Science and Engineering 5. Berlin: Springer (ISBN 978-3-540-68094-9/hbk). xi, 470 p. (2007).
The book is translation of the German edition (2004; Zbl 1038.81004). It presents numerical techniques used in molecular dynamics and shows how to write a program in molecular dynamics using a parallel computer with distributed memory. The mathematical model used by the authors is the Newton’s second law applied to a great number of particles interacting by means of short-range or long-range force fields and potentials. The basic methods of study are the linked cell method, the particle mesh method, and the \(P^3M\) method and its variants. These methods allow to study a large scale of phenomena: physical, biological, chemical or material-structural.
The book contains nine chapters followed by a “Prospects” chapter and five appendices. Chapter 1 “Computer simulation – a key technology” presents the fundamentals. In chapter 2 “From Schrödinger equation to molecular dynamics” the authors derive the clasical molecular dynamics of particle system from the principles of quantum mechanics. Chapter 3 “The linked cell method for short-range potentials” presents the method and applies it to some examples. Chapter 4 “Parallelization” gives other examples of parallel implementation of the linked cell method. The content of chapter 5 “Extensions to more complex potentials and molecules” is clearly expressed in its title. In chapter 6 “Time integration method” the authors give an overview of methods for time integration. Chapters 7 and 8 entitled as “Mesh-based methods for long-range potentials” and “Tree algorithms for long-range potentials” present different methods for the computation of long-range force fields. Chapter 9 “Applications from biochemistry and biophysics” contains applications of above methods to biochemical and biophysical phenomena. Finally, in“Prospects” the authors discuss some possibilities to improve the theory in some directions.
The book contains nine chapters followed by a “Prospects” chapter and five appendices. Chapter 1 “Computer simulation – a key technology” presents the fundamentals. In chapter 2 “From Schrödinger equation to molecular dynamics” the authors derive the clasical molecular dynamics of particle system from the principles of quantum mechanics. Chapter 3 “The linked cell method for short-range potentials” presents the method and applies it to some examples. Chapter 4 “Parallelization” gives other examples of parallel implementation of the linked cell method. The content of chapter 5 “Extensions to more complex potentials and molecules” is clearly expressed in its title. In chapter 6 “Time integration method” the authors give an overview of methods for time integration. Chapters 7 and 8 entitled as “Mesh-based methods for long-range potentials” and “Tree algorithms for long-range potentials” present different methods for the computation of long-range force fields. Chapter 9 “Applications from biochemistry and biophysics” contains applications of above methods to biochemical and biophysical phenomena. Finally, in“Prospects” the authors discuss some possibilities to improve the theory in some directions.
Reviewer: Vasile Ionescu (Bucureşti)
MSC:
76-02 | Research exposition (monographs, survey articles) pertaining to fluid mechanics |
76M28 | Particle methods and lattice-gas methods |
82-02 | Research exposition (monographs, survey articles) pertaining to statistical mechanics |
82-08 | Computational methods (statistical mechanics) (MSC2010) |