A Practical Introduction to the Simulation of Molecular Systems

About this book

Molecular simulation is a powerful tool in materials science, physics, chemistry and biomolecular fields. This updated edition provides a pragmatic introduction to a wide range of techniques for the simulation of molecular systems at the atomic level. The first part concentrates on methods for calculating the potential energy of a molecular system, with new chapters on quantum chemical, molecular mechanical and hybrid potential techniques. The second part describes methods examining conformational, dynamical and thermodynamical properties of systems, covering techniques including geometry-optimization, normal-mode analysis, molecular dynamics, and Monte Carlo simulation. Using Python, the second edition includes numerous examples and program modules for each simulation technique, allowing the reader to perform the calculations and appreciate the inherent difficulties involved in each.

Contents

Preface to the second edition; Preface to the first edition; 1. Preliminaries; 2. Chemical models and representations; 3. Coordinates and co-ordinate manipulations; 4. Quantum chemical models; 5. Molecular mechanics; 6. Hybrid potentials; 7. Finding stationary points and reaction paths; 8. Normal mode analysis; 9. Molecular dynamics simulations I; 10. More on non-bonding interactions; 11. Molecular dynamics simulations II; 12. Monte Carlo simulations; Appendix 1 - The pDynamo library; Appendix 2 - Mathematical appendix; Appendix 3 - Solvent boxes and solvated molecules; Bibliography.

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Biography

Martin J. Field is Group Leader of the Laboratoire de Dynamique Moleculaire at the Institut de Biologie Structurale - Jean-Pierre Ebel, Grenoble. He was awarded his PhD in quantum chemistry from the University of Manchester, UK, in 1985. His areas of research include using molecular modeling and simulation techniques to study biological problems more specifically, his current interests are in the development and application of hybrid potential techniques to study enzymatic reaction mechanisms and other condensed phase processes.