A practical introduction to the simulation of molecular systems:
Gespeichert in:
| 1. Verfasser: | |
|---|---|
| Format: | Buch |
| Sprache: | English |
| Veröffentlicht: |
Cambridge [u.a.]
Cambridge Univ. Press
2007
|
| Ausgabe: | 2. ed., 1. publ. |
| Schlagworte: | |
| Online-Zugang: | Table of contents only Publisher description Contributor biographical information Inhaltsverzeichnis |
| Beschreibung: | Previous ed.: 1999. Includes bibliographical references (p. 307-325) and indexes |
| Beschreibung: | XI, 339 S. graph. Darst. 26 cm |
| ISBN: | 9780521852524 |
Internformat
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| 100 | 1 | |a Field, Martin J. |e Verfasser |4 aut | |
| 245 | 1 | 0 | |a A practical introduction to the simulation of molecular systems |c Martin J. Field |
| 250 | |a 2. ed., 1. publ. | ||
| 264 | 1 | |a Cambridge [u.a.] |b Cambridge Univ. Press |c 2007 | |
| 300 | |a XI, 339 S. |b graph. Darst. |c 26 cm | ||
| 336 | |b txt |2 rdacontent | ||
| 337 | |b n |2 rdamedia | ||
| 338 | |b nc |2 rdacarrier | ||
| 500 | |a Previous ed.: 1999. | ||
| 500 | |a Includes bibliographical references (p. 307-325) and indexes | ||
| 650 | 7 | |a Modèles chimiques - Simulation par ordinateur |2 ram | |
| 650 | 7 | |a Molécules - Modèles |2 ram | |
| 650 | 4 | |a Molecules |x Models |x Computer simulation | |
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Datensatz im Suchindex
| _version_ | 1804137310267113472 |
|---|---|
| adam_text | Contents
Preface
to the first edition page
ix
Preface to the second edition
xi
1
Preliminaries
1
1.1
Introduction
1
1.2
Python
2
1.3
Object-oriented programming
5
1.4
The pDynamo library
8
1.5
Notation and units
9
2
Chemical models and representations
14
2.1
Introduction
14
2.2
The System class
14
2.3
Example
1 17
2.4
Common molecular representations
18
2.5
Example
2 27
3
Coordinates and coordinate manipulations
31
3.1
Introduction
31
3.2
Connectivity
31
3.3
Internal coordinates
35
3.4
Example
3 38
3.5
Miscellaneous transformations
41
3.6
Superimposing structures
45
3.7
Example
4 47
4
Quantum chemical models
51
4.1
Introduction
51
4.2
The Born-Oppenheimer approximation
51
4.3
Strategies for obtaining energies on a potential energy surface
53
vi
Contents
4.4
Molecular orbital
methods
54
4.5
The Hartree-Fock approximation
56
4.6
Analysis of the charge density
67
4.7
Example
5 70
4.8
Derivatives of the potential energy
74
4.9
Example
6 78
5
Molecular mechanics
81
5.1
Introduction
81
5.2
Typical empirical energy functions
81
5.3
Calculating a molecular mechanics energy
93
5.4
Example
7 101
5.5
Parametrizing potential energy functions
103
5.6
Soft constraints
105
6
Hybrid potentials
110
6.1
Introduction
110
6.2
Combining QC and MM potentials
110
6.3
Example
8 114
6.4
Covalent bonds between QC and MM atoms
116
6.5
Example
9 120
7
Finding stationary points and reaction paths on potential
energy surfaces
122
7.1
Introduction
122
7.2
Exploring potential energy surfaces
122
7.3
Locating minima
126
7.4
Example
10 129
7.5
Locating saddle points
130
7.6
Example
11 134
7.7
Following reaction paths
136
7.8
Example
12 139
7.9
Determining complete reaction paths
140
7.10
Example
13 144
8
Normal mode analysis
148
8.1
Introduction
148
8.2
Calculation of the normal modes
148
8.3
Rotational and translational modes
153
8.4
Generating normal mode trajectories
156
8.5
Example
14 158
8.6
Calculation of thermodynamic quantities
161
8.7
Example
15 165
Contents
vii
9
Molecular
dynamics
simulations
I
170
9.1
Introduction
170
9.2
Molecular dynamics
170
9.3
Example
16 178
9.4
Trajectory analysis
182
9.5
Example
17 184
9.6
Simulated annealing
186
9.7
Example
18 189
10
More on non-bonding interactions
195
10.1
Introduction
195
10.2
Cutoff methods for the calculation of non-bonding interactions
195
10.3
Example
19 205
10.4
Including an environment
209
10.5
Periodic boundary conditions
212
10.6
Example
20 215
10.7 Ewald
summation techniques
217
10.8
Fast methods for the evaluation of non-bonding interactions
223
11
Molecular dynamics simulations II
225
11.1
Introduction
225
11.2
Analysis of molecular dynamics trajectories
225
11.3
Example
21 233
11.4
Temperature and pressure control in molecular dynamics
simulations
235
11.5
Example
22 244
11.6
Calculating free energies: umbrella sampling
246
11.7
Examples
23
and
24 252
11.8
Speeding up simulations
258
12
Monte Carlo simulations
262
12.1
Introduction
262
12.2
The Metropolis Monte Carlo method
262
12.3
Monte Carlo simulations of molecules
266
12.4
Example
25 277
12.5
Calculating free energies: statistical perturbation theory
280
12.6
Example
26 286
Appendix
1
The pDynamo library
294
Appendix
2
Mathematical appendix
298
A2.1 The eigenvalues and eigenvectors of a matrix
298
A2.2 The method of
Lagrange
multipliers
300
viii Contents
Appendix 3 Solvent
boxes and solvated molecules
302
A3.1 Example
27 302
A3.2 Example
28 305
Bibliography
307
Author index
326
Subject index
330
|
| adam_txt |
Contents
Preface
to the first edition page
ix
Preface to the second edition
xi
1
Preliminaries
1
1.1
Introduction
1
1.2
Python
2
1.3
Object-oriented programming
5
1.4
The pDynamo library
8
1.5
Notation and units
9
2
Chemical models and representations
14
2.1
Introduction
14
2.2
The System class
14
2.3
Example
1 17
2.4
Common molecular representations
18
2.5
Example
2 27
3
Coordinates and coordinate manipulations
31
3.1
Introduction
31
3.2
Connectivity
31
3.3
Internal coordinates
35
3.4
Example
3 38
3.5
Miscellaneous transformations
41
3.6
Superimposing structures
45
3.7
Example
4 47
4
Quantum chemical models
51
4.1
Introduction
51
4.2
The Born-Oppenheimer approximation
51
4.3
Strategies for obtaining energies on a potential energy surface
53
vi
Contents
4.4
Molecular orbital
methods
54
4.5
The Hartree-Fock approximation
56
4.6
Analysis of the charge density
67
4.7
Example
5 70
4.8
Derivatives of the potential energy
74
4.9
Example
6 78
5
Molecular mechanics
81
5.1
Introduction
81
5.2
Typical empirical energy functions
81
5.3
Calculating a molecular mechanics energy
93
5.4
Example
7 101
5.5
Parametrizing potential energy functions
103
5.6
Soft constraints
105
6
Hybrid potentials
110
6.1
Introduction
110
6.2
Combining QC and MM potentials
110
6.3
Example
8 114
6.4
Covalent bonds between QC and MM atoms
116
6.5
Example
9 120
7
Finding stationary points and reaction paths on potential
energy surfaces
122
7.1
Introduction
122
7.2
Exploring potential energy surfaces
122
7.3
Locating minima
126
7.4
Example
10 129
7.5
Locating saddle points
130
7.6
Example
11 134
7.7
Following reaction paths
136
7.8
Example
12 139
7.9
Determining complete reaction paths
140
7.10
Example
13 144
8
Normal mode analysis
148
8.1
Introduction
148
8.2
Calculation of the normal modes
148
8.3
Rotational and translational modes
153
8.4
Generating normal mode trajectories
156
8.5
Example
14 158
8.6
Calculation of thermodynamic quantities
161
8.7
Example
15 165
Contents
vii
9
Molecular
dynamics
simulations
I
170
9.1
Introduction
170
9.2
Molecular dynamics
170
9.3
Example
16 178
9.4
Trajectory analysis
182
9.5
Example
17 184
9.6
Simulated annealing
186
9.7
Example
18 189
10
More on non-bonding interactions
195
10.1
Introduction
195
10.2
Cutoff methods for the calculation of non-bonding interactions
195
10.3
Example
19 205
10.4
Including an environment
209
10.5
Periodic boundary conditions
212
10.6
Example
20 215
10.7 Ewald
summation techniques
217
10.8
Fast methods for the evaluation of non-bonding interactions
223
11
Molecular dynamics simulations II
225
11.1
Introduction
225
11.2
Analysis of molecular dynamics trajectories
225
11.3
Example
21 233
11.4
Temperature and pressure control in molecular dynamics
simulations
235
11.5
Example
22 244
11.6
Calculating free energies: umbrella sampling
246
11.7
Examples
23
and
24 252
11.8
Speeding up simulations
258
12
Monte Carlo simulations
262
12.1
Introduction
262
12.2
The Metropolis Monte Carlo method
262
12.3
Monte Carlo simulations of molecules
266
12.4
Example
25 277
12.5
Calculating free energies: statistical perturbation theory
280
12.6
Example
26 286
Appendix
1
The pDynamo library
294
Appendix
2
Mathematical appendix
298
A2.1 The eigenvalues and eigenvectors of a matrix
298
A2.2 The method of
Lagrange
multipliers
300
viii Contents
Appendix 3 Solvent
boxes and solvated molecules
302
A3.1 Example
27 302
A3.2 Example
28 305
Bibliography
307
Author index
326
Subject index
330 |
| any_adam_object | 1 |
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| edition | 2. ed., 1. publ. |
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| id | DE-604.BV023068373 |
| illustrated | Illustrated |
| index_date | 2024-07-02T19:31:56Z |
| indexdate | 2024-07-09T21:10:16Z |
| institution | BVB |
| isbn | 9780521852524 |
| language | English |
| lccn | 2007299634 |
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| physical | XI, 339 S. graph. Darst. 26 cm |
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| publishDateSearch | 2007 |
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| spelling | Field, Martin J. Verfasser aut A practical introduction to the simulation of molecular systems Martin J. Field 2. ed., 1. publ. Cambridge [u.a.] Cambridge Univ. Press 2007 XI, 339 S. graph. Darst. 26 cm txt rdacontent n rdamedia nc rdacarrier Previous ed.: 1999. Includes bibliographical references (p. 307-325) and indexes Modèles chimiques - Simulation par ordinateur ram Molécules - Modèles ram Molecules Models Computer simulation Molekülsystem (DE-588)4507233-4 gnd rswk-swf Molekül (DE-588)4039972-2 gnd rswk-swf Computersimulation (DE-588)4148259-1 gnd rswk-swf Molekülsystem (DE-588)4507233-4 s Computersimulation (DE-588)4148259-1 s DE-604 Molekül (DE-588)4039972-2 s 1\p DE-604 http://www.loc.gov/catdir/enhancements/fy0803/2007299634-t.html Table of contents only http://www.loc.gov/catdir/enhancements/fy0803/2007299634-d.html Publisher description http://www.loc.gov/catdir/enhancements/fy0803/2007299634-b.html Contributor biographical information Digitalisierung UB Bayreuth application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=016271543&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis 1\p cgwrk 20201028 DE-101 https://d-nb.info/provenance/plan#cgwrk |
| spellingShingle | Field, Martin J. A practical introduction to the simulation of molecular systems Modèles chimiques - Simulation par ordinateur ram Molécules - Modèles ram Molecules Models Computer simulation Molekülsystem (DE-588)4507233-4 gnd Molekül (DE-588)4039972-2 gnd Computersimulation (DE-588)4148259-1 gnd |
| subject_GND | (DE-588)4507233-4 (DE-588)4039972-2 (DE-588)4148259-1 |
| title | A practical introduction to the simulation of molecular systems |
| title_auth | A practical introduction to the simulation of molecular systems |
| title_exact_search | A practical introduction to the simulation of molecular systems |
| title_exact_search_txtP | A practical introduction to the simulation of molecular systems |
| title_full | A practical introduction to the simulation of molecular systems Martin J. Field |
| title_fullStr | A practical introduction to the simulation of molecular systems Martin J. Field |
| title_full_unstemmed | A practical introduction to the simulation of molecular systems Martin J. Field |
| title_short | A practical introduction to the simulation of molecular systems |
| title_sort | a practical introduction to the simulation of molecular systems |
| topic | Modèles chimiques - Simulation par ordinateur ram Molécules - Modèles ram Molecules Models Computer simulation Molekülsystem (DE-588)4507233-4 gnd Molekül (DE-588)4039972-2 gnd Computersimulation (DE-588)4148259-1 gnd |
| topic_facet | Modèles chimiques - Simulation par ordinateur Molécules - Modèles Molecules Models Computer simulation Molekülsystem Molekül Computersimulation |
| url | http://www.loc.gov/catdir/enhancements/fy0803/2007299634-t.html http://www.loc.gov/catdir/enhancements/fy0803/2007299634-d.html http://www.loc.gov/catdir/enhancements/fy0803/2007299634-b.html http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=016271543&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
| work_keys_str_mv | AT fieldmartinj apracticalintroductiontothesimulationofmolecularsystems |