分子体系模拟应用入门 第2版 英文【2025|PDF|Epub|mobi|kindle电子书版本百度云盘下载】

分子体系模拟应用入门 第2版 英文PDF格式电子书版下载

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1 Preliminaries1

1.1 Introduction1

1.2 Python2

1.3 Object-oriented programming5

1.4 The pDynamo library8

1.5 Notation and units9

2 Chemical models and representations14

2.1 Introduction14

2.2 The System class14

2.3 Example 117

2.4 Common molecular representations18

2.5 Example 227

3 Coordinates and coordinate manipulations31

3.1 Introduction31

3.2 Connectivity31

3.3 Internal coordinates35

3.4 Example 338

3.5 Miscellaneous transformations41

3.6 Superimposing structures45

3.7 Example 447

4 Quantum chemical models51

4.1 Introduction51

4.2 The Born-Oppenheimer approximation51

4.3 Strategies for obtaining energies on a potential energy surface53

4.4 Molecular orbital methods54

4.5 The Hartree-Fock approximation56

4.6 Analysis of the charge density67

4.7 Example 570

4.8 Derivatives of the potential energy74

4.9 Example 678

5 Molecular mechanics81

5.1 Introduction81

5.2 Typical empirical energy functions81

5.3 Calculating a molecular mechanics energy93

5.4 Example 7101

5.5 Parametrizing potential energy functions103

5.6 Soft constraints105

6 Hybrid potentials110

6.1 Introduction110

6.2 Combining QC and MM potentials110

6.3 Example 8114

6.4 Covalent bonds between QC and MM atoms116

6.5 Example 9120

7 Finding stationary points and reaction paths on potential energy surfaces122

7.1 Introduction122

7.2 Exploring potential energy surfaces122

7.3 Locating minima126

7.4 Example 10129

7.5 Locating saddle points130

7.6 Example 11134

7.7 Following reaction paths136

7.8 Example 12139

7.9 Determining complete reaction paths140

7.10 Example 13144

8 Normal mode analysis148

8.1 Introduction148

8.2 Calculation of the normal modes148

8.3 Rotational and translational modes153

8.4 Generating normal mode trajectories156

8.5 Example 14158

8.6 Calculation of thermodynamic quantities161

8.7 Example 15165

9 Molecular dynamics simulations Ⅰ170

9.1 Introduction170

9.2 Molecular dynamics170

9.3 Example 16178

9.4 Trajectory analysis182

9.5 Example 17184

9.6 Simulated annealing186

9.7 Example 18189

10 More on non-bonding interactions195

10.1 Introduction195

10.2 Cutoff methods for the calculation of non-bonding interactions195

10.3 Example 19205

10.4 Including an environment209

10.5 Periodic boundary conditions212

10.6 Example 20215

10.7 Ewald summation techniques217

10.8 Fast methods for the evaluation of non-bonding interactions223

11 Molecular dynamics simulations Ⅱ225

11.1 Introduction225

11.2 Analysis of molecular dynamics trajectories225

11.3 Example 21233

11.4 Temperature and pressure control in molecular dynamics simulations235

11.5 Example 22244

11.6 Calculating free energies:umbrella sampling246

11.7 Examples 23 and 24252

11.8 Speeding up simulations258

12 Monte Carlo simulations262

12.1 Introduction262

12.2 The Metropolis Monte Carlo method262

12.3 Monte Carlo simulations of molecules266

12.4 Example 25277

12.5 Calculating free energies:statistical perturbation theory280

12.6 Example 26286

Appendix 1 The pDynamo library294

Appendix 2 Mathematical appendix298

A2.1 The eigenvalues and eigenvectors of a matrix298

A2.2 The method of Lagrange multipliers300

Appendix 3 Solvent boxes and solvated molecules302

A3.1 Example 27302

A3.2 Example 28305

Bibliography307

Author index326

Subject index330