Preface to the first edition Preface to the second edition 1 Preliminaries 1.1 Introduction 1.2 Python 1.3 Object-oriented programming 1.4 The pDynamo library 1.5 Notation and units 2 Chemical models and representations 2.1 Introduction 2.2 The System class 2.3 Example 1 2.4 Common molecular representations 2.5 Example 2 3 Coordinates and coordinate manipulations 3.1 Introduction 3.2 Connectivity 3.3 Internal coordinates 3.4 Example 3 3.5 Miscellaneous transformations 3.6 Superimposing structures 3.7 Example 4 4 Quantum chemical models 4.1 Introduction 4.2 The Born-Oppenheimer approximation 4.3 Strategies for obtaining energies on a potential energy surface 4.4 Molecular orbital methods 4.5 The Hartree-Fock approximation 4.6 Analysis of the charge density 4.7 Example 5 4.8 Derivatives of the potential energy 4.9 Example 6 5 Molecular mechanics 5.1 Introduction 5.2 Typical empirical energy functions 5.3 Calculating a molecular mechanics energy 5.4 Example 7 5.5 Parametrizing potential energy functions 5.6 Soft constraints Hybrid potentials 6.1 Introduction 6.2 Combining QC and MM potentials 6.3 Example 8 6.4 Covalent bonds between QC and MM atoms 6.5 Example 9 Finding stationary points and reaction paths on potential energy surfaces 7.1 Introduction 7.2 Exploring potential energy surfaces 7.3 Locating minima 7.4 Example 10 7.5 Locating saddle points 7.6 Example 11 7.7 Following reaction paths 7.8 Example 12 7.9 Determining complete reaction paths 7.10 Example 13 8 Normal mode analysis 8.1 Introduction 8.2 Calculation of the normal modes 8.3 Rotational and translational modes 8.4 Generating normal mode trajectories 8.5 Example 14 8.6 Calculation of thermodynamic quantities 8.7 Example 15 …… Appendix 1 The pDynamo library Appendix 2 Mathematical appendix Appendix 3 Solvent boxes and solvated molecules
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