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RSS订阅The art of Molecular Dynamics Simulations ,2nd Edition,Rapaport
分子动力学模拟最为经典的一本书。
Contents:
1 Introduction 1
1.1 Historical background 1
1.2 Computer simulation 2
1.3 Molecular dynamics 4
1.4 Organization 8
1.5 Further reading 10
2 Basic molecular dynamics 11
2.1 Introduction 11
2.2 Soft-disk fluid 11
2.3 Methodology 18
2.4 Programming 20
2.5 Results 34
2.6 Further study 43
3 Simulating simple systems 44
3.1 Introduction 44
3.2 Equations of motion 44
3.3 Potential functions 46
3.4 Interaction computations 49
3.5 Integration methods 60
3.6 Initial state 67
3.7 Performance measurements 74
3.8 Trajectory sensitivity 77
3.9 Further study 82
v
vi Contents
4 Equilibrium properties of simple fluids 83
4.1 Introduction 83
4.2 Thermodynamic measurements 84
4.3 Structure 90
4.4 Packing studies 96
4.5 Cluster analysis 112
4.6 Further study 118
5 Dynamical properties of simple fluids 120
5.1 Introduction 120
5.2 Transport coefficients 120
5.3 Measuring transport coefficients 124
5.4 Space–time correlation functions 134
5.5 Measurements 145
5.6 Further study 152
6 Alternative ensembles 153
6.1 Introduction 153
6.2 Feedback methods 154
6.3 Constraint methods 165
6.4 Further study 174
7 Nonequilibrium dynamics 176
7.1 Introduction 176
7.2 Homogeneous and inhomogeneous systems 176
7.3 Direct measurement 177
7.4 Modified dynamics 188
7.5 Further study 198
8 Rigid molecules 199
8.1 Introduction 199
8.2 Dynamics 200
8.3 Molecular construction 216
8.4 Measurements 222
8.5 Rotation matrix representation 232
8.6 Further study 243
9 Flexible molecules 245
9.1 Introduction 245
9.2 Description of molecule 245
9.3 Implementation details 247
9.4 Properties 251
9.5 Modeling structure formation 256
Contents vii
9.6 Surfactant models 257
9.7 Surfactant behavior 262
9.8 Further study 266
10 Geometrically constrained molecules 267
10.1 Introduction 267
10.2 Geometric constraints 267
10.3 Solving the constraint problem 270
10.4 Internal forces 278
10.5 Implementation details 286
10.6 Measurements 291
10.7 Further study 294
11 Internal coordinates 296
11.1 Introd
2009-03-10
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