The Art of Molecular Dynamics SimulationIn this Second Edition an extensive series of detailed case studies introduces the reader to solutions to a variety of problems connected with the way molecular interactions and motions determine the properties of matter. The methods are widely used in studying phenomena involving everything from the simplest of liquids to highly complex molecules such as proteins. In addition to a significant amount of new material, this edition features completely rewritten software. First Edition Hb (1996): 0-521-44561-2 First Edition Pb (1996): 0-521-59942-3 |
Contents
Introduction | 1 |
12 Computer simulation | 2 |
13 Molecular dynamics Foundations | 4 |
14 Organization | 8 |
15 Further reading | 10 |
Basic molecular dynamics | 11 |
23 Methodology | 18 |
24 Programming | 20 |
107 Further study | 294 |
Internal coordinates | 296 |
113 Kinematic and dynamic relations | 298 |
114 Recursive description of dynamics | 299 |
115 Solving the recursion equations | 308 |
116 Implementation details | 317 |
117 Measurements | 322 |
118 Further study | 325 |
25 Results | 34 |
26 Further study | 43 |
Simulating simple systems | 44 |
33 Potential functions | 46 |
34 Interaction computations | 49 |
35 Integration methods | 60 |
36 Initial state | 67 |
37 Performance measurements | 74 |
38 Trajectory sensitivity | 77 |
39 Further study | 82 |
Equilibrium properties of simple fluids | 83 |
42 Thermodynamic measurements | 84 |
43 Structure | 90 |
44 Packing studies | 96 |
45 Cluster analysis | 112 |
46 Further study | 118 |
Dynamical properties of simple fluids | 120 |
53 Measuring transport coefficients Direct evaluation of diffusion | 124 |
54 Spacetime correlation functions | 134 |
55 Measurements | 145 |
56 Further study | 152 |
Alternative ensembles | 153 |
62 Feedback methods | 154 |
63 Constraint methods | 165 |
64 Further study | 174 |
Nonequilibrium dynamics | 176 |
73 Direct measurement Viscous flow | 177 |
74 Modified dynamics | 188 |
75 Further study | 198 |
Rigid molecules | 199 |
82 Dynamics | 200 |
83 Molecular construction | 216 |
84 Measurements | 222 |
85 Rotation matrix representation | 232 |
86 Further study | 243 |
Flexible molecules | 245 |
93 Implementation details | 247 |
94 Properties | 251 |
95 Modeling structure formation | 256 |
96 Surfactant models | 257 |
97 Surfactant behavior | 262 |
98 Further study | 266 |
Geometrically constrained molecules | 267 |
103 Solving the constraint problem | 270 |
104 Internal forces | 278 |
105 Implementation details | 286 |
106 Measurements | 291 |
Manybody interactions | 326 |
123 Em beddedatom approach | 332 |
124 Further study | 343 |
Longrange interactions | 344 |
132 Ewald method | 345 |
133 Treecode approach | 359 |
134 Fastmultipole method | 365 |
135 Implementing the fastmultipole method | 373 |
136 Results | 386 |
137 Further study | 389 |
Step potentials | 391 |
142 Computational approach | 392 |
143 Event management | 403 |
144 Properties | 411 |
145 Generalizations | 414 |
146 Further study | 417 |
Timedependent phenomena | 418 |
153 Thermal convection | 420 |
154 Obstructed flow | 429 |
155 Further study | 435 |
Granular dynamics | 436 |
163 Vibrating granular layer | 439 |
164 Wave patterns | 443 |
165 Further study | 445 |
Algorithms for supercomputers | 446 |
173 Techniques for parallel processing | 447 |
174 Distributed computation | 450 |
175 Sharedmemory parallelism Overview | 467 |
176 Techniques for vector processing | 473 |
177 Further study | 480 |
More about software | 481 |
183 Allocating arrays | 487 |
184 Utility functions | 488 |
185 Organizing input data | 495 |
186 Configuration snapshot files | 498 |
187 Managing extensive computations | 500 |
188 Header files | 504 |
The future | 505 |
192 Limits of growth | 506 |
193 Visualization and interactivity | 507 |
194 Coda | 508 |
Appendix | 509 |
| 519 | |
| 532 | |
| 535 | |
Colophon | |
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Common terms and phrases
AllocArrays AllocMem angle array atoms bond cDev cell cellList chain chainLen collision computation ComputeForces constraints coordinates define deltaT density dihedral angle DO_MOL energy equations of motion evaluated evTree fcVal flist fluid fopen force fprintf fp function initial initUcell input data integration interaction lattice leapfrog leapfrog integration linear M_PI matrix measurements method mol n].rv molecular dynamics molecules mpCell mSite multipole expansions NameI NameR NDIM neighbor list nLayer nMol nValCorr pairs periodic boundaries Phys potential problem processor quaternions radial distribution function rCut region region.x rotation rotation matrix rrCut rri3 simulation SingleStep sitesMol sizeof soft-sphere sqrt stepAvg stepCount stepEquil stepLimit structure tBuf tCell temperature timesteps transport coefficients typedef struct values variables varL VComp VDiv VDot VecR vector vector processing velocity vFac VLenSq dr VMul void VProd VScale VSet VSub dr VVSAdd mol vvSum VZero