A Practical Introduction to the Simulation of

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. This is a valuable resource for researchers and graduate students wanting to know how to use atomic-scale molecular simulations. Supplementary material, including the program library and technical information, available through www.cambridge.org/9780521852524.

Martin J. Field is Group Leader of the Laboratoire de Dynamique Moleculaire at the Institut de Biologie Structurale - Jean - Pierre Ebel, Grenoble

Preface to the first edition	p. ix
Preface to the second edition	p. xi
Preliminaries	p. 1
Introduction	p. 1
Python	p. 2
Object-oriented programming	p. 5
The pDynamo library	p. 8
Notation and units	p. 9
Chemical models and representations	p. 14
Introduction	p. 14
The System class	p. 14
Example 1	p. 17
Common molecular representations	p. 18
Example 2	p. 27
Coordinates and coordinate manipulations	p. 31
Introduction	p. 31
Connectivity	p. 31
Internal coordinates	p. 35
Example 3	p. 38
Miscellaneous transformations	p. 41
Superimposing structures	p. 45
Example 4	p. 47
Quantum chemical models	p. 51
Introduction	p. 51
The Born-Oppenheimer approximation	p. 51
Strategies for obtaining energies on a potential energy surface	p. 53
Molecular orbital methods	p. 54
The Hartree-Fock approximation	p. 56
Analysis of the charge density	p. 67
Example 5	p. 70
Derivatives of the potential energy	p. 74
Example 6	p. 78
Molecular mechanics	p. 81
Introduction	p. 81
Typical empirical energy functions	p. 81
Calculating a molecular mechanics energy	p. 93
Example 7	p. 101
Parametrizing potential energy functions	p. 103
Soft constraints	p. 105
Hybrid potentials	p. 110
Introduction	p. 110
Combining QC and MM potentials	p. 110
Example 8	p. 114
Covalent bonds between QC and MM atoms	p. 116
Example 9	p. 120
Finding stationary points and reaction paths on potential energy surfaces	p. 122
Introduction	p. 122
Exploring potential energy surfaces	p. 122
Locating minima	p. 126
Example 10	p. 129
Locating saddle points	p. 130
Example 11	p. 134
Following reaction paths	p. 136
Example 12	p. 139
Determining complete reaction paths	p. 140
Example 13	p. 144
Normal mode analysis	p. 148
Introduction	p. 148
Calculation of the normal modes	p. 148
Rotational and translational modes	p. 153
Generating normal mode trajectories	p. 156
Example 14	p. 158
Calculation of thermodynamic quantities	p. 161
Example 15	p. 165
Molecular dynamics simulations I	p. 170
Introduction	p. 170
Molecular dynamics	p. 170
Example 16	p. 178
Trajectory analysis	p. 182
Example 17	p. 184
Simulated annealing	p. 186
Example 18	p. 189
More on non-bonding interactions	p. 195
Introduction	p. 195
Cutoff methods for the calculation of non-bonding interactions	p. 195
Example 19	p. 205
Including an environment	p. 209
Periodic boundary conditions	p. 212
Example 20	p. 215
Ewald summation techniques	p. 217
Fast methods for the evaluation of non-bonding interactions	p. 223
Molecular dynamics simulations II	p. 225
Introduction	p. 225
Analysis of molecular dynamics trajectories	p. 225
Example 21	p. 233
Temperature and pressure control in molecular dynamics simulations	p. 235
Example 22	p. 244
Calculating free energies: umbrella sampling	p. 246
Examples 23 and 24	p. 252
Speeding up simulations	p. 258
Monte Carlo simulations	p. 262
Introduction	p. 262
The Metropolis Monte Carlo method	p. 262
Monte Carlo simulations of molecules	p. 266
Example 25	p. 277
Calculating free energies: statistical perturbation theory	p. 280
Example 26	p. 286
The pDynamo library	p. 294
Mathematical appendix	p. 298
The eigenvalues and eigenvectors of a matrix	p. 298
The method of Lagrange multipliers	p. 300
Solvent boxes and solvated molecules	p. 302
Example 27	p. 302
Example 28	p. 305
Bibliography	p. 307
Author index	p. 326
Subject index	p. 330
Table of Contents provided by Ingram. All Rights Reserved.

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A Practical Introduction to the Simulation of Molecular Systems

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