Molecular Dynamics

Note: Supplemental materials are not guaranteed with Rental or Used book purchases.

ISBN: 9780444829108 | 0444829105
Cover: Hardcover
Copyright: 4/22/1999

Buy New

Print on Demand: 2-4 Weeks. This item cannot be cancelled or returned.

$536.86
eBook

Available Instantly

Online: 1825 Days

Downloadable: Lifetime Access

$742.50

The latest developments in quantum and classical molecular dynamics, related techniques, and their applications to several fields of science and engineering. Molecular simulations include a broad range of methodologies such as Monte Carlo, Brownian dynamics, lattice dynamics, and molecular dynamics (MD).Features of this book:- Presents advances in methodologies, introduces quantum methods and lists new techniques for classical MD- Deals with complex systems: biomolecules, aqueous solutions, ice and clathrates, liquid crystals, polymers- Provides chemical reactions, interfaces, catalysis, surface phenomena and solidsAlthough the book is not formally divided into methods and applications, the chapters are arranged starting with those that discuss new algorithms, methods and techniques, followed by several important applications.

Methods of incorporating quantum mechanical calculations into molecular dynamics simulations

(30)

Aatto Laaksonen

Yaoquan Tu

Introduction

(1)

Combined QM/MM simulation methods

(12)

Partitioning of the system into QM and MM parts

(1)

Background

(1)

Model

(2)

Partitioning the QM and MM parts across chemical bonds

(1)

QM/MM coupling

(1)

Simple coupling

(1)

Coupling including the polarization from the MM part

(2)

QM/MM coupling and the fluctuating charge model

(2)

Computational aspects

(1)

Implementation

(1)

Integral calculation

(1)

Parameterization

(1)

Ab Initio molecular dynamics

(5)

Introduction

(1)

Car-Parrinello method

(4)

Path-integral molecular dynamics

(2)

Future prospects

(10)

Classical molecular dynamics simulations with quantum degrees of freedom

(30)

J. Brickmann

U. Schmitt

Introductikon

(3)

Approximate solutions to the time-dependent Schrodinger equation

(3)

The multi configuration time-dependent self consistent field approximation (MCTDSCF)

(1)

The time-dependent self consistent field (TDSCF) approximation

(1)

Quantum-classical mixed mode equations

(4)

The quantum trajectory model

(2)

Mixed quantum-classical dynamics

(1)

The classically based separable potential (CSP) approximation

(1)

Hamilton-Jacobi formulation of the mixed quantum-classical equations

(3)

The numerical integration of the mixed mode equations

(3)

The Liouville formalism

(2)

Multiple time step propagation scheme

(1)

Selected applications

(7)

A quantum oscillator in a bath of classical particles

(4)

The photodissociation/recombination dynamics of I2 in an Ar matrix: Wave packet propagation

(3)

Conclusion

(7)

Spatial structure in molecular liquids

(38)

Peter G. Kusalik

Aatto Laaksonen

Igor M. Svishchev

Introduction

(4)

Computational details

(4)

Calculation of SDFs

(1)

Rigid molecules

(1)

Flexible molecules

(1)

Spherical-polar coordinates

(1)

Cartesian coordinates

(1)

Visualization of SDFs

(1)

Pure liquids

(14)

Dipolar spheres

(2)

Water

(7)

Methanol

(1)

Other non-aqueous liquids

(4)

Solutions

(6)

Water/ethanol

(3)

Water/methylamine

(1)

Water/acetonitrile

(1)

Water/benzene

(1)

DNA in aqueous solution

(1)

Carbohydrates solution

(1)

Into the future

(10)

Appendix

(9)

Thermodynamic integration along coexistence lines

(30)

David A. Kofke

Jeffrey A. Henning

Evaluation of phase equilibria by molecular simulation

(2)

Gibbs-Duhem integration

101

(5)

Bubble-point and dew-point coexistence lines

106

(13)

Introduction

106

(2)

Semigrand ensemble

108

(1)

Integration scheme

109

(5)

Application

114

(3)

Results

117

(2)

Residue curve maps

119

(5)

Introduction

119

(3)

Method

122

(2)

Concluding remarks

124

(5)

Energy minimization by smoothing techniques: a survey

129

(58)

S. Schelstraete

W. Schepens

H. Verschelde

Introduction

129

(5)

A note on notations

131

(1)

Test cases and applications

131

(3)

Parametric interaction modification methods

134

(5)

Scaling of the exponents in the Lennard-Jones potential

134

(1)

Shift method

135

(1)

Distance scaling

136

(1)

Regularization of the Lennard-Jones potential

137

(2)

Convolution methods

139

(8)

Diffusion equation method (DEM).

140

(5)

Method of bad derivatives

145

(2)

Quantum methods

147

(5)

Time-independent Schrodinger equation

148

(1)

SCMTF

149

(1)

Imaginary time Schrodinger equation with Gaussian wave packets

149

(2)

Quantum annealing

151

(1)

Statistical mechanics methods -- evolution equations

152

(8)

Gaussian phase packet (GPP)

153

(3)

Gaussian density annealing (GDA)

156

(2)

Smoluchowski dynamics

158

(1)

General evolution equation method

159

(1)

Statistical mechanics methods -- variational methods

160

(13)

Effective potential method

161

(2)

Effective diffused potential (EDP)

163

(5)

Effective potential with a top-hat distribution

168

(2)

Gaussian packet states (GPS)

170

(1)

A general variational approach to smoothing

171

(2)

Other methods

173

(14)

Convex global underrestimator (CGU)

173

(1)

Multi-copy or locally enhanced sampling

174

(2)

Energy embedding/relaxation of dimensionality

176

(11)

Ab initio and DFT for the strength of classical molecular dynamics simulations

187

(44)

Jorge M. Seminario

Introduction

187

(1)

Quantum calculations

188

(2)

The conventional ab initio techniques

190

(4)

Hartree Fock method

190

(1)

Configuration interaction

191

(2)

Perturbation theory

193

(1)

Coupled cluster methods

194

(1)

Density functional methods

194

(4)

Advantges of working with the density instead of the wave function

196

(1)

Exchange-correlation functionals

197

(1)

B3LYP, B3PW91, especial functionals

198

(1)

Applications of DFT and ab initio methods

198

(14)

Weak bonds and interactions, special bonds

198

(1)

Atoms and very small clusters

199

(1)

Very small molecules

200

(2)

Transition metals

202

(3)

Study of defects

205

(1)

Ferromagnetism spin

206

(1)

Relativistic calculations

207

(2)

Pseudopotential, effective core potentials

209

(1)

Extended systems

210

(1)

Metallic clusters

210

(1)

Catalysis

211

(1)

Corrosion

212

(1)

Topological analysis

212

(1)

Molecular dynamics

212

(19)

Rotation barriers

212

(1)

Liquids

212

(1)

Interfaces

213

(1)

FUERZA procedure for evaluation of intramolecular force fields

214

(2)

The combined DFT/MD procedure

216

(1)

Intramolecular force field

216

(1)

Intermolecular force field

216

(1)

Box construction

217

(1)

Heating and equilibration

218

(1)

Features of the combined DFT/MD method

218

(13)

Large scale parallel molecular dynamics simulations

231

(50)

Fredrik Hedman

Aatto Laaksonen

Introduction

231

(2)

``Large scale ``vs large scale

233

(3)

The simulation scale phase space of MD

233

(2)

Do we really need large scale simulations?

235

(1)

High performance computers and MD

236

(11)

Software aspects

236

(1)

Parallel computer models

237

(3)

Programming models and languages

240

(1)

Performance models

240

(2)

Hardware aspects

242

(1)

Organization of memory

243

(3)

Type of processing node

246

(1)

Directions not explored

246

(1)

Software and hardware interaction

246

(1)

Hints for further walkabouts

247

(1)

Large scale parallel MD

247

(16)

MD and the 90/10 rule

247

(1)

General software and hardware considerations

248

(3)

Cost of calculating the interactions

251

(1)

Algorithms for large--scale MD

252

(1)

Short-range interactions

252

(3)

Long-range interactions

255

(2)

Implementation and other issues

257

(1)

Algorithms for parallel MD

257

(1)

Task queue

258

(1)

Replicated data and systolic loops

258

(3)

Spatial decomposition

261

(1)

Hints for further walkabouts

262

(1)

Trends and challenges

263

(18)

Appendix

265

(1)

MD in a nut-shell

265

(2)

Boundary conditions

267

(1)

Interactions in simple atomic systems.

268

(1)

Empirical force fields

269

(12)

Combined MD simulation-NMR relaxation studies of molecular motion and intermolecular interactions

281

(44)

Michael Odelius

Aatto Laaksonen

Introduction and background

281

(5)

Nuclear spins as probes for molecular information

283

(2)

Theoretical models

285

(1)

Intra-and intermolecular NMR relaxation

285

(1)

Nuclear spin relaxation processes

286

(2)

Models

288

(3)

MD models

289

(1)

Time correlation functions

290

(1)

MD simulations and NMR relaxation

291

(23)

Dipole-Dipole mechanism

291

(3)

Intermolecular dipole-dipole relaxation

294

(1)

Paramagnetic relaxation

295

(1)

Proton relaxation in Ni2+ (aq)

296

(3)

Quadrupolar relaxation mechanism

299

(3)

Calculations of liquid state QCCs

302

(2)

Intermolecular quadrupolar relaxation

304

(4)

Chemical shielding anisotropy

308

(1)

13C relaxation in O=C=S

309

(2)

Spin-rotation relaxation

311

(1)

Spin-rotation and chemical shielding

312

(1)

Scalar relaxation

313

(1)

Intermolecular scalar relaxation of HF (aq.)

314

(1)

Conclusions

314

(11)

Basic formal NMR theory

315

(1)

Bloch equations

315

(1)

Master equations

316

(9)

Transport properties of liquid crystals via molecular dynamics simulation

325

(38)

Sten Sarman

Introduction

325

(2)

Basic theory

327

(9)

Linear transport processes

327

(1)

Rigid body dynamics

328

(1)

Nonequilibrium molecular dynamics

329

(2)

Gauss' principle and thermostats

331

(2)

Order parameters directors and angular velocities

333

(1)

Director constraint algorithm

334

(2)

Nonequilibrium molecular dynamics algorithms

336

(6)

Heat flow algorithms

336

(4)

Equations of motion for shear flow

340

(2)

Flow properties of liquid crystals

342

(7)

Simulation studies of liquid crystal shear flow

349

(5)

Conclusion

354

(9)

Appendix I

358

(2)

Appendix II

360

(3)

Interaction potentials for small molecules

363

(68)

F.M. Floris

A. Tani

Introduction

363

(2)

Basic interaction forces

365

(4)

Ab initio potentials

369

(7)

The supermolecular method

369

(3)

Perturbative methods

372

(4)

Potential models

376

(13)

Potential models and properties

376

(3)

Functional forms and types of potential

379

(4)

Atomic and phase transferability

383

(1)

Non additivity

384

(5)

Water-water potentials

389

(16)

Empirical and semi-empirical effective models

392

(4)

Empirical and semi-empirical polarizable models

396

(4)

Ab initio models

400

(5)

Ion-water potentials

405

(26)

Structural and thermodynamic properties

405

(7)

Dynamic properties

412

(1)

Ion-ion interactions

413

(18)

Ab initio and molecular dynamics studies of cation-water interactions

431

(40)

P.B. Balbuena

L. Wang

T. Li

P.A. Derosa

Introduction

431

(4)

DFT results

435

(19)

Selection of basis set

436

(3)

Structure and binding energies

439

(1)

Monohydrates

439

(1)

Hexahydrates

440

(4)

Potential functions

444

(1)

Pairwise additive potential functions

444

(6)

Non-additive terms: effects of polarization in the potential function

450

(2)

Potential functions of dissociation of hexahydrate complexes

452

(2)

Molecular dynamics simulations

454

(7)

Conclusions

461

(10)

Interpretation of inelastic neutron scattering spectra for water ice by lattice and molecular dynamic simulations

471

(62)

Jichen Li

John Tomkinson

Introduction

471

(15)

Inelastic neutron scattering techniques

474

(7)

Some instrumental considerations

481

(1)

Lattice dynamic calculations

482

(4)

Molecular dynamic simulation of neutron spectra

486

(7)

Equipartition theorem

487

(2)

Anharmonicity and temperature effects

489

(1)

Size effects and the calculated DOS

490

(3)

The energy resolution and intensity statistics

493

(1)

Water-water potentials

493

(8)

Water clusters and polarisable potentials

497

(2)

Validating water potentials

499

(2)

Neutron vibrational spectra of the exotic ices

501

(7)

Simulations of neutron spectra of ice Ih

508

(14)

Lattice dynamic simulations by use of the classic potentials

512

(4)

Molecular dynamic simulations

516

(1)

Rigid molecule potentials

517

(2)

Non-rigid water potential

519

(2)

Polarisable potentials

521

(1)

Summary

522

(1)

The two strengths of hydrogen bond model

522

(7)

The variation of the two force constants

523

(2)

Effects of proton disordering

525

(2)

The anomalies of water and ice

527

(1)

Melting and boiling temperature

527

(1)

High heat capacity

527

(1)

High surface tension

527

(2)

Polymorphism of ice

529

(1)

Discussion

529

(4)

Stability and dynamics of ice and clathrate hydrate

533

(46)

Hideki Tanaka

Introduction

533

(3)

Structure of ices and clathrate hydrates

536

(6)

Hexagonal and cubic ices

536

(3)

Clathrate hydrates

539

(3)

Partition function and free energy

542

(11)

Free energy calculation

542

(3)

Van der Waals and Platteeuw theory

545

(4)

Anisotropy of propane and ethane guest molecules

549

(2)

Evaluation of anharmonic free energy

551

(1)

Grandcanonical MC simulation

551

(2)

Thermodynamic stability of clathrate hydrates

553

(9)

Relative stability of empty hydrates to ice

553

(1)

Free energy of cage occupancy

554

(4)

Anharmonic free energy

558

(1)

Grandcanonical MC simulation

559

(3)

Calculation of free energy and volume

562

(17)

Free energy minimization

563

(2)

Gruneisen relation

565

(1)

Thermodynamic stability of Ice Ih and Ic

565

(1)

Thermal expansivity of Ice Ih

566

(8)

Thermal expansivity of clathrate hydrate

574

(5)

Molecular dynamics studies of physically adsorbed fluid

579

(50)

William Steele

Introduction

579

(2)

Algorithms

581

(7)

Potential energies

588

(5)

Thermodynamics and structure

593

(18)

Isotherm simulations

593

(3)

Other thermodynamic properties

596

(2)

Wetting

598

(3)

Freezing of absorbed gases

601

(10)

Dynamics

611

(18)

Motions of individual molecules

611

(2)

Self-diffusion

613

(4)

Diffusion and viscous flow in high density adsorbed phases

617

(1)

Phase separation dynamics

618

(1)

Tribology

619

(10)

Molecular dynamics of thin films under shear

629

(32)

Shaoyi Jiang

James F. Belak

Introduction

629

(1)

Potential models

630

(7)

Modeling fluids

631

(3)

Modeling the walls

634

(3)

Temperature control

637

(2)

Simulation methods

639

(1)

Properties

640

(14)

Flow boundary condition

641

(5)

Friction

646

(5)

Shear viscosity

651

(3)

Summary

654

(7)

Molecular dynamics simulations of chemical reactions at liquid interfaces

661

(42)

Ilan Benjamin

Introduction

661

(1)

Methods

662

(13)

Potential energy functions

662

(3)

Boundary conditions

665

(3)

Equilibrium simulations

668

(1)

Density profiles

668

(1)

Inhomogeneous molecular properties

669

(2)

Surface tension

671

(1)

Surface potential

671

(1)

Free energy

672

(2)

Non-equilibrium simulations

674

(1)

The character of the interfacial region

675

(9)

Large scale structures

675

(2)

Microscopic structure and dynamics

677

(4)

General behavior of solute molecules at interfaces

681

(3)

Charge transfer reactions

684

(12)

Preliminaries

685

(2)

Equilibrium

687

(1)

Background

687

(4)

Results for charge transfer at liquid interfaces

691

(3)

Non-equilibrium

694

(2)

Conclusions

696

(7)

Molecular dynamics simulation of copper using CHARMM: methodological considerations and initial results

703

(34)

Howard E. Alper

Peter Politzer

Introduction

703

(3)

Method

706

(3)

Testing of method

709

(14)

Reimaging

710

(1)

Determination of the τT and τp parameters for NPT simulations

710

(1)

Convergence of the simulations

711

(6)

Basic properties of the system: pressure, temperature, and total energy

717

(1)

Other properties.

717

(5)

The effect of cutoffs

722

(1)

Summary of results

723

(8)

300K

723

(4)

1000K

727

(2)

Comparison of results at 300K and 1000K

729

(2)

Conclusions and future plans

731

(6)

Dynamic Monte Carlo simulations of oscillatory heterogeneous catalytic reactions.

737

(48)

R.J. Gelten

R.A. van Santen

A. P.J. Jansen

Introduction

737

(2)

Theory

739

(21)

The derivation of the master equation

739

(5)

The relation between the master equation and macroscopic rate equations

744

(1)

Desorption without lateral interactions

745

(1)

Bimolecular reactions

746

(3)

Improving the macroscopic reaction rate equations..

749

(2)

Using Monte Carlo to solve the master equations

751

(1)

An integral formulation of the master equation and the variable step size method

751

(2)

Time-dependent transition probabilities and the first reaction method

753

(2)

The random-selection method

755

(1)

The efficiency of VSSM, FRM, RSM

756

(1)

A comparison with other methods

757

(3)

Applications of the Monte Carlo technique

760

(18)

The Ziff-Gulari-Barshad model

760

(1)

Monte Carlo results

760

(2)

Mean-field approximations

762

(2)

CO oxidation on Pt (100)

764

(1)

Model

765

(1)

Reaction fronts and oscillations.

766

(6)

Stability of the oscillations

772

(1)

Spatio-temporal pattern formation

773

(2)

Mean-field results

775

(3)

Summary

778

(7)

Polymerization of rodlike molecules

785

(44)

D.V. Khakhar

Introduction

785

(3)

Dynamics of rodlike polymers

788

(3)

Dilute solutions

789

(1)

Semi-dilute solutions

790

(1)

Experimental studies of polymerization kinetics

791

(5)

Theoretical analyses: Smoluchowski approach

796

(7)

Mathematical formulation

796

(3)

Dilute solutions

799

(1)

Semi-dilute solutions

800

(1)

Comparison to experimental results

801

(2)

Multiparticle brownian dynamics

803

(3)

Pairwise brownian dynamics

806

(16)

Theory

807

(1)

Finite domain correction

808

(3)

Finite rates of reaction

811

(2)

Isotropic translational diffusion

813

(1)

Spherical reaction site with reactive patches

813

(3)

Reaction between rodlike molecules in dilute solutions

816

(2)

Anisotropic diffusion

818

(1)

Reaction between rodlike molecules in semidilute solutions.

819

(2)

Discussion

821

(1)

Conclusions

822

(7)

Potential energy and free energy surfaces of floppy systems. Ab initio calculations and molecular dynamics simulations

829

(30)

Pavel Hobza

Introduction

829

(2)

Strategy of calculations

831

(9)

Quantum chemical calculations

831

(1)

Calculation of the interaction energy

831

(2)

Empirical potential

833

(1)

Benzene...Arn clusters

833

(2)

Nucleic acid base pairs

835

(1)

Molecular dynamics

836

(1)

Quenching technique

837

(2)

Statistical thermodynamic treatment

839

(1)

Results and discussion

840

(15)

Benzene...Arn

840

(1)

Verification of the Benzene...Ar empirical potential.

840

(1)

PES and FES of Benzene...Arn clusters

841

(1)

Benzene...Ar2

841

(1)

Benzene...Arn (n=3 and 5)

842

(1)

Benzene...Ar7.

842

(1)

Benzene...Ar8

843

(1)

Dissociation temperatures of the clusters studied

844

(1)

Structure of the benzene...Arn clusters

844

(1)

Concluding remarks

844

(1)

Nucleic acid base pairs

845

(1)

Rigid rotor -- harmonic oscillator -- ideal gas thermodynamic characteristics

845

(3)

Uracil dimer

848

(1)

Potential energy surface

848

(2)

Free energy surface

850

(1)

Rigid rotor-harmonic oscillator-ideal gas approximation.

850

(1)

NVE ensemble

851

(1)

N1-methyluracil dimer

852

(2)

Concluding remarks

854

(1)

Conclusions

855

(4)

Ways and means to enhance the configurational sampling of small peptides in aqueous solution in molecular dynamics simulations

859

(40)

Frederico Nardi

Rebecca C. Wade

Introduction

859

(2)

Application to Ala-cisPro-Tyr

861

(1)

Conformational search algorithms

862

(5)

Systematic search

862

(1)

Probabilistic search

863

(1)

Application to Ala-cisPro-Tyr

864

(1)

Data base analysis

865

(1)

Systematic search

866

(1)

Simulation sampling techniques

867

(24)

Increase the sampling time scales

868

(1)

Run a long simulation

868

(1)

Application to Ala-cisPro-Tyr

868

(2)

Run multiple simulations

870

(1)

Application to Ala-cisPro-Tyr

871

(2)

Use multiple timesteps

873

(1)

Reduce the number of degrees of freedom

873

(1)

Use implicit solvent model

873

(1)

Use simplified solute model

873

(1)

Move along principal low-frequency degrees of freedom

874

(1)

Multi-copy MD

874

(1)

Modify the free energy surface

874

(1)

Modify force field

874

(1)

Modify temperature

875

(1)

Add predefined biasing function

875

(1)

Umbrella sampling

875

(1)

Free energy computation

876

(2)

Application to Ala-cisPro-Tyr

878

(1)

Biasing the rotamers

879

(4)

Validation of the biasing potential on pentane in vacuum

883

(3)

Application to Ala-cisPro-Tyr

886

(1)

Add evolving biasing function

886

(1)

Local elevation

886

(1)

Configurational flooding

887

(1)

Iterative Weighted Histogram Analysis Method (WHAM)

887

(2)

Application to Ala-cisPro-Tyr

889

(1)

Promising methods

890

(1)

Conclusion

891

(8)

Molecular dynamics of pectic substances

899

(34)

B. Manunza

S. Deiana

C. Gessa

Introduction

899

(4)

Theoretical methods

903

(4)

Force fields for carbohydrates

907

(2)

Model calculations on α-D-galacturono di- and tri-saccharides

909

(1)

Molecular dynamics calculations of poly-galacturonic (PGA) acid chains and poly-galacturonate complexes with Na+ and Ca2+

909

(15)

Interchain interactions

910

(1)

One chain system

911

(1)

Two chains system.

912

(1)

Three chains systems

912

(1)

The PGA-water system

913

(4)

The PGA-Na and PGA-Ca water systems

917

(4)

The PGA-Ca2+-Na+-water system

921

(3)

Conclusions

924

(9)

Index

933

Please wait while the item is added to your bag...

FREE SHIPPING

Amazon no longer offers textbook rentals. We do!

Molecular Dynamics

Summary

Table of Contents

Supplemental Materials