# Basic Concepts And Trends In Ab Initio Molecular Dynamics

M. Tuckerman

Published 2004 · Physics

The field of ab initio molecular dynamics, in which finite temperature molecular dynamics trajectories are generated using forces obtained from electronic structure calculations performed “on the fly”, is a rapidly evolving and growing technology that allows chemical processes in condensed phases to be studied in an accurate and unbiased way. This article is intended to present the basics of the ab initio molecular dynamics method and to highlight some recent trends. Beginning with a derivation of the method from the Born-Oppenheimer approximation, issues including the density functional representation of electronic structure, basis sets, calculation of observables, and the Car-Parrinello extended Lagrangian algorithm and extensions of the latter are discussed.

This paper references

10.1021/AR010104U

Quantum theory of dissociative chemisorption on metal surfaces.

G. Kroes (2002)

10.1063/1.1321309

New τ-dependent correlation functional combined with a modified Becke exchange

E. Proynov (2000)

10.1103/PhysRevLett.88.086403

First-principles theory of the EPR g tensor in solids: defects in quartz.

C. Pickard (2002)

10.1063/1.3048320

Quantum Mechanics and Path Integrals

R. Feynman (1965)

10.1147/rd.453.0397

DFT-based molecular dynamics as a new tool for computational biology: First applications and perspective

W. Andreoni (2001)

10.1103/PhysRevB.43.1993

Efficient pseudopotentials for plane-wave calculations.

Troullier (1991)

10.1126/SCIENCE.1056991

Autoionization in Liquid Water

P. Geissler (2001)

10.1103/PHYSREVLETT.88.166402

Nonadiabatic Car-Parrinello molecular dynamics.

N. Doltsinis (2002)

10.1021/JP010008A

Protonic Defects in Hydrogen Bonded Liquids: Structure and Dynamics in Ammonia and Comparison with Water†

Y. Liu (2001)

10.1063/1.471771

Efficient and general algorithms for path integral Car-Parrinello molecular dynamics

M. Tuckerman (1996)

10.1103/PHYSREVB.57.14133

Dynamic structure factor of vitreous silica from first principles: Comparison to neutron-inelastic-scattering experiments

A. Pasquarello (1998)

10.1016/S0038-1098(96)00723-5

From silicon to RNA: The coming of age of ab initio molecular dynamics

M. Parrinello (1997)

10.1021/JA990913X

First principles study of propene polymerization in Ziegler-Natta heterogeneous catalysis

M. Boero (2000)

10.1103/PhysRevB.50.4954

Implementation of gradient-corrected exchange-correlation potentials in Car-Parrinello total-energy calculations.

White (1994)

10.1016/0009-2614(93)87016-V

Structures of small water clusters using gradient-corrected density functional theory

K. Laasonen (1993)

10.1103/PHYSREVB.64.224205

Structural properties of molten silicates from ab initio molecular-dynamics simulations: Comparison between C a O − A l 2 O 3 − S i O 2 and SiO 2

M. Benoit (2001)

10.1021/j100091a022

Structural Study of (H2O)20 and (H2O)21H+ Using Density Functional Methods

K. Laasonen (1994)

10.1080/00268979909483112

The electrostatic properties of water molecules in condensed phases: an ab initio study

L. D. Site (1999)

10.1103/PhysRevB.47.1651

Theory of polarization of crystalline solids.

King-Smith (1993)

10.1007/978-94-009-9027-2_2

Density-functional theory of atoms and molecules

R. Parr (1989)

10.1103/PhysRev.136.B864

THE INHOMOGENEOUS ELECTRON GAS.

P. Hohenberg (1964)

10.1063/1.462066

Density-functional thermochemistry. I. The effect of the exchange-only gradient correction

Axel D. Becke (1992)

10.1007/978-94-011-1679-4

Computer Simulation in Chemical Physics

M. Allen (1993)

10.1088/0953-8984/14/20/201

Why are insulators insulating and metals conducting

Raffaele Resta (2002)

10.1007/BF01312185

Ab initio path-integral molecular dynamics

D. Marx (1994)

10.1103/PHYSREVLETT.80.3388

NMR Chemical Shifts in Hard Carbon Nitride Compounds

Y. Yoon (1998)

10.1103/PhysRevB.56.12847

Maximally localized generalized Wannier functions for composite energy bands

Nicola Marzari (1997)

10.1103/PhysRevB.48.14646

Unconstrained minimization approach for electronic computations that scales linearly with system size.

Ordejón (1993)

10.1103/PHYSREVB.60.2941

SIGNATURE OF SURFACE STATES ON NMR CHEMICAL SHIFTS : A THEORETICAL PREDICTION

F. Mauri (1999)

10.1016/S0039-6028(01)01551-5

Catalysis and corrosion: the theoretical surface-science context

C. Stampfl (2002)

10.1021/JP020866M

Ab Initio Molecular Dynamics Investigation of the Concentration Dependence of Charged Defect Transport in Basic Solutions via Calculation of the Infrared Spectrum

Z. Zhu (2002)

10.1038/367601b0

Fast pulsations in Wolf–Rayet stars

P. Martinez (1994)

10.1103/PhysRevLett.55.2471

Unified approach for molecular dynamics and density-functional theory.

Car (1985)

10.1063/1.462100

A novel discrete variable representation for quantum mechanical reactive scattering via the S-matrix Kohn method

D. Colbert (1992)

10.1021/ja00104a073

Ab initio molecular dynamics study of hydrochloric acid in water

K. Laasonen (1994)

10.1063/1.1453397

A new reciprocal space based treatment of long range interactions on surfaces

P. Mináry (2002)

10.1063/1.477923

A reciprocal space based method for treating long range interactions in ab initio and force-field-based calculations in clusters

G. J. Martyna (1999)

10.1021/JA972367I

First Principles Molecular Dynamics Study of Ziegler−Natta Heterogeneous Catalysis

M. Boero (1998)

10.1103/PhysRevB.41.7892

Soft self-consistent pseudopotentials in a generalized eigenvalue formalism.

Vanderbilt (1990)

10.1063/1.469654

Ab initio molecular dynamics simulation of the solvation and transport of hydronium and hydroxyl ions in water

M. Tuckerman (1995)

10.1103/PhysRevA.52.1096

Adiabatic density-functional perturbation theory.

Gonze (1995)

Modern methods and algorithms of quantum chemistry

J. Grotendorst (2000)

10.1016/S0009-2614(97)00930-5

Ab initio infrared spectrum of liquid water

P. L. Silvestrelli (1997)

10.1063/1.469201

Integrating the Car–Parrinello equations. III. Techniques for ultrasoft pseudopotentials

Jürg Hutter (1995)

10.1103/PhysRevA.38.3098

Density-functional exchange-energy approximation with correct asymptotic behavior.

Becke (1988)

10.1103/PhysRevLett.48.1425

Efficacious Form for Model Pseudopotentials

L. Kleinman (1982)

10.1103/PhysRevB.50.17953

Projector augmented-wave method.

Blöchl (1994)

10.1021/JP962513R

Ab initio study of aqueous hydrochloric acid

K. Laasonen (1997)

10.1038/17579

The nature of the hydrated excess proton in water

D. Marx (1999)

10.1103/PhysRevLett.80.1800

Quantum-Mechanical Position Operator in Extended Systems

Raffaele Resta (1998)

10.1103/PhysRevB.48.2081

Born-Oppenheimer molecular-dynamics simulations of finite systems: Structure and dynamics of (H2O)2.

Barnett (1993)

10.1007/978-94-011-1679-4_8

First-principles Molecular Dynamics

G. Galli (1993)

10.1103/PhysRevB.45.13244

Accurate and simple analytic representation of the electron-gas correlation energy.

Perdew (1992)

10.1080/00018736200101282

Neutron scattering studies of liquid diffusion

P. A. Egelstaff (1962)

10.1103/PhysRevB.43.6796

Implementation of ultrasoft pseudopotentials in ab initio molecular dynamics.

Laasonen (1991)

10.1063/1.1473659

Car–Parrinello molecular dynamics simulation of liquid water: New results

S. Izvekov (2002)

10.1103/PhysRevB.41.12264

Ghost states for separable, norm-conserving, Iab initioP pseudopotentials.

Gonze (1990)

10.1103/PHYSREVLETT.82.3308

Water Molecule Dipole in the Gas and in the Liquid Phase

P. L. Silvestrelli (1999)

10.1103/PHYSREVLETT.79.2340

{ital Ab initio} NMR Chemical Shift of Diamond, Chemical-Vapor-Deposited Diamond, and Amorphous Carbon

F. Mauri (1997)

Computer simulation in chemical physics, NATO ASI Series C

M. P. Allen (1993)

10.1103/PhysRevB.47.10142

Car-Parrinello molecular dynamics with Vanderbilt ultrasoft pseudopotentials.

Laasonen (1993)

10.1103/PHYSREVLETT.79.1766

DYNAMICAL CHARGE TENSORS AND INFRARED SPECTRUM OF AMORPHOUS SIO2

A. Pasquarello (1997)

10.1103/PhysRevLett.76.4246

Magnetic susceptibility of insulators from first principles.

Mauri (1996)

10.1103/PhysRevB.39.13120

Density-functional approach to nonlinear-response coefficients of solids.

Gonze (1989)

10.1007/978-3-642-56080-4_16

A New Reciprocal Space Based Method for Treating Long Range Interactions in Ab Initio and Force-Field Based Calculations for Surfaces, Wires, and Clusters

M. Tuckerman (2002)

10.1103/PHYSREVLETT.87.265501

Dissociation of water under pressure.

E. Schwegler (2001)

10.1021/JP010780D

A First Principles Exploration of a Variety of Active Surfaces and Catalytic Sites in Ziegler−Natta Heterogeneous Catalysis

M. Boero (2001)

10.1016/S0009-2614(99)00851-9

Density-functional study of liquid methanol

E. Tsuchida (1999)

10.1016/S0009-2614(98)00286-3

The dissociation mechanism of H2O in water studied by first-principles molecular dynamics

B. L. Trout (1998)

10.1088/0953-8984/14/11/303

Recent progress in linear scaling ab initio electronic structure techniques

D. Bowler (2002)

10.1016/0009-2614(85)80121-4

Solution of self-consistent field electronic structure equations by a pseudospectral method☆

R. Friesner (1985)

10.1080/00268979650026640

Ab initio molecular dynamics study of dilute hydrofluoric acid

K. Laasonen (1996)

10.1103/PHYSREVB.59.9703

Maximally localized Wannier functions for simulations with supercells of general symmetry

P. L. Silvestrelli (1999)

10.1126/SCIENCE.275.5301.817

On the Quantum Nature of the Shared Proton in Hydrogen Bonds

M. Tuckerman (1997)

10.1016/S0009-2614(99)00683-1

Catalysis of the reaction HCl+HOCl→H2O+Cl2 on an ice surface

Z. Liu (1999)

10.1063/1.1457432

A dynamical correlation functional

N. Handy (2002)

10.1088/0953-8984/12/8A/317

Solvated excess protons in water: quantum effects on the hydration structure

D. Marx (2000)

10.1063/1.1448491

On the use of the adiabatic molecular dynamics technique in the calculation of free energy profiles

Lula Rosso (2002)

10.1063/1.1473811

A general framework for discrete variable representation basis sets

R. Littlejohn (2002)

10.1021/JA003145E

Ab initio molecular dynamics-based assignment of the protonation state of pepstatin A/HIV-1 protease cleavage site.

S. Piana (2001)

10.1080/002689797170220

A hybrid Gaussian and plane wave density functional scheme

Gerald Lippert (1997)

10.1021/JP004243P

First-Principles Molecular Dynamics Study of the Rupture Processes of a Bulklike Polyethylene Knot

A. M. Saitta (2001)

10.1038/nature00797

The nature and transport mechanism of hydrated hydroxide ions in aqueous solution

M. Tuckerman (2002)

10.1063/1.463940

Nosé–Hoover chains: The canonical ensemble via continuous dynamics

G. J. Martyna (1992)

10.1002/1097-461X(2000)80:6<1172::AID-QUA4>3.0.CO;2-E

First‐principles molecular dynamics simulations of models for the myoglobin active center

C. Rovira (2000)

10.1021/JA991376J

Evolution of Fragments Formed at the Rupture of a Knotted Alkane Molecule

A. M. Saitta (1999)

10.1103/PHYSREVLETT.81.1235

Ab Initio Infrared Absorption Study of the Hydrogen-Bond Symmetrization in Ice

M. Bernasconi (1998)

10.1126/SCIENCE.275.5308.1925

Origin of the High-Frequency Doublet in the Vibrational Spectrum of Vitreous SiO2

Johannes Sarnthein (1997)

10.1021/JP002619T

Ab Initio Molecular Dynamics Study of the Superacid System SbF5/HF Solution

Dongsup Kim and (2000)

10.1063/1.475496

Ab initio study of gas-phase sulphuric acid hydrates containing 1 to 3 water molecules

H. Arstila (1998)

10.1038/19935

Influence of a knot on the strength of a polymer strand

A. M. Saitta (1999)

10.1063/1.1424928

Empirical correction to density functional theory for van der Waals interactions

Q. Wu (2002)

10.1007/978-3-642-56080-4

Computational Methods for Macromolecules: Challenges and Applications

T. Schlick (2002)

10.1063/1.471957

Ab initio molecular dynamics simulation of liquid water: Comparison of three gradient‐corrected density functionals

M. Sprik (1996)

10.1103/PhysRevB.47.4863

Ab initio studies on the structural and dynamical properties of ice.

Lee (1993)

10.1021/j100013a001

Full Configuration Interaction Molecular Dynamics of Na2 and Na3

Z. Liu (1995)

10.1080/00268970010018431

Left-right correlation energy

N. Handy (2001)

10.1103/PhysRevLett.73.2599

Ab initio molecular dynamics with excited electrons.

Alavi (1994)

10.1016/S0010-4655(99)00208-8

Quantum dynamics via adiabatic ab initio centroid molecular dynamics

D. Marx (1999)

10.1016/S0167-2738(99)00154-X

The role of quantum effects and ionic defects in high-density ice

M. Benoit (1999)

10.1007/978-1-4613-2389-1

Dynamic Light Scattering

R. Pécora (1985)

10.1063/1.479855

Polyethylene under tensil load: Strain energy storage and breaking of linear and knotted alkanes probed by first-principles molecular dynamics calculations

A. M. Saitta (1999)

10.1016/S0006-3495(96)79321-9

Ab initio molecular dynamics study of proton transfer in a polyglycine analog of the ion channel gramicidin A.

D. Sagnella (1996)

10.1103/PhysRevA.39.3761

Exchange holes in inhomogeneous systems: A coordinate-space model.

Becke (1989)

10.1103/PhysRevB.63.245101

All-electron magnetic response with pseudopotentials: NMR chemical shifts

C. Pickard (2001)

10.1039/B001167N

All-electron ab-initio molecular dynamics

Matthias Krack (2000)

10.1103/PhysRevB.26.4199

Pseudopotentials that work: From H to Pu

G. Bachelet (1982)

10.1002/1521-3838(200207)21:2<97::AID-QSAR97>3.0.CO;2-6

Introduction to Density-Functional Theory and ab-Initio Molecular Dynamics

R. Car (2002)

10.1063/1.1496457

Ab initio molecular dynamics study of proton mobility in liquid methanol

Joseph A Morrone (2002)

10.1021/jp960480+

Ab Initio Molecular Dynamics Simulations

M. Tuckerman (1996)

10.1103/PhysRevB.37.785

Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density.

Lee (1988)

10.1063/1.479451

A comparison of methods for the calculation of NMR chemical shifts

Thomas Gregor (1999)

10.1063/1.479194

Simulation studies of liquid ammonia by classical ab initio, classical, and path-integral molecular dynamics

M. Diraison (1999)

10.1103/PhysRev.140.A1133

Self-Consistent Equations Including Exchange and Correlation Effects

W. Kohn (1965)

10.1063/1.1446022

Functionals of quantities other than the electron density: Approximations to the exchange energy

M. Ernzerhof (2002)

10.1016/0009-2614(94)00494-3

Properties of supercritical water: an ab initio simulation

E. Fois (1994)

10.1016/0009-2614(90)80078-R

Some useful discrete variable representations for problems in time-dependent and time-independent quantum mechanics

J. T. Muckerman (1990)

10.1103/PhysRevB.50.4316

Electronic-structure calculations and molecular-dynamics simulations with linear system-size scaling.

Mauri (1994)

10.1002/(SICI)1097-461X(1999)73:2<209::AID-QUA14>3.0.CO;2-B

Ab initio molecular dynamics studies of a synthetic biomimetic model of galactose oxidase

U. Rothlisberger (1999)

10.1021/JA020350G

First-principles study of aqueous hydroxide solutions.

B. Chen (2002)

10.1063/1.471221

Ab initio path integral molecular dynamics: Basic ideas

D. Marx (1996)

10.1021/JA9808447

Intermediate range order and bonding character in disordered network-forming systems

C. Massobrio (1999)

10.1021/JP000040P

First-Principles Molecular Dynamics Simulations of H2O on α-Al2O3 (0001)

K. C. H. and (2000)

10.1021/JP994056V

A Density Functional Theory Study of a Silica-Supported Zirconium Monohydride Catalyst for Depolymerization of Polyethylene

Jens Jørgen Mortensen and (2000)

10.1103/PhysRevLett.77.3865

Generalized Gradient Approximation Made Simple.

Perdew (1996)

10.1038/32609

Tunnelling and zero-point motion in high-pressure ice

M. Benoit (1998)

10.1021/JA991961K

NMR chemical shifts of ice and liquid water: The effects of condensation

Bernd G. Pfrommer (2000)

10.1021/JA972935U

Ab initio molecular dynamics study of the reaction of water with formaldehyde in sulfuric acid solution.

M. Sprik (1998)

10.1021/JP982623T

Quantum Nuclear ab Initio Molecular Dynamics Study of Water Wires

H. S. Mei (1998)

10.1088/0031-8949/1996/T66/014

Ab-initio simulation of phase transformations under pressure

M. Bernasconi (1996)

10.1016/S0009-2614(00)00381-X

Ab initio analysis of proton transfer dynamics in (H2O)3H

P. Geissler (2000)

10.1103/PHYSREVB.61.10040

General and efficient algorithms for obtaining maximally localized Wannier functions

G. Berghold (2000)

10.1088/0953-8984/8/47/036

Ab initio molecular dynamics simulation of liquids and solutions

M. Sprik (2000)

10.1088/0953-8984/14/50/202

Ab initio molecular dynamics: basic concepts, current trends and novel applications

M. Tuckerman (2002)

10.1103/PhysRevLett.69.462

Ab initio studies on high pressure phases of ice.

Lee (1992)

10.1016/S0010-4655(99)00390-2

Grid methods and Hilbert space basis for simulations of quantum dynamics

S. Gu'erin (1999)

10.1063/1.448462

Generalized discrete variable approximation in quantum mechanics

J. Light (1985)

10.1021/ja00540a008

An empirical valence bond approach for comparing reactions in solutions and in enzymes

A. Warshel (1980)

10.1103/PHYSREVLETT.78.887

Structure and hyperfine parameters of E'(1) centers in a-quartz and in vitreous SiO2

M. Boero (1997)

10.1103/RevModPhys.66.899

Macroscopic polarization in crystalline dielectrics: the geometric phase approach

Raffaele Resta (1994)

10.1016/S0006-3495(01)75711-6

Influence of the heme pocket conformation on the structure and vibrations of the Fe-CO bond in myoglobin: a QM/MM density functional study.

C. Rovira (2001)

10.1021/j100016a003

Ab initio molecular dynamics simulation of the solvation and transport of H3O+ and OH- ions in water

M. Tuckerman (1995)

10.1103/PhysRevLett.69.3547

Large scale electronic structure calculations.

Galli (1992)

10.1016/S0010-4655(99)00251-9

An high performance Fortran implementation of a Tight-Binding Molecular Dynamics simulation

B. D. Martino (1999)

10.1016/S0301-0104(00)00129-4

Computation of the pK of liquid water using coordination constraints

M. Sprik (2000)

10.1103/PhysRevB.45.9413

Adiabaticity in first-principles molecular dynamics.

Blöchl (1992)

10.1103/PhysRevLett.58.1861

Green's-function approach to linear response in solids.

Baroni (1987)

10.1080/00268979000101451

Molecular dynamics without effective potentials via the Car-Parrinello approach

D. Remler (1990)

10.1103/PhysRevA.31.1695

Canonical dynamics: Equilibrium phase-space distributions.

Hoover (1985)

10.1103/PHYSREVB.62.R4786

Si-O-Si bond-angle distribution in vitreous silica from first-principles 29 Si NMR analysis

F. Mauri (2000)

10.1126/SCIENCE.282.5387.265

The chemistry of water on alumina surfaces: reaction dynamics from first principles

Hass (1998)

10.1063/1.1312830

Generalized variational density functional perturbation theory

A. Putrino (2000)

10.1063/1.480951

Simulation of delocalized exchange by local density functionals

A. D. Becke (2000)

10.1021/JP002807J

A New ab-Initio Approach for NMR Chemical Shifts in Periodic Systems

D. Sebastiani (2001)

10.1007/978-1-4757-9975-0

Density Functional Theory

E. Gross (1990)

10.1103/PhysRevLett.77.5300

Ab Initio Theory of NMR Chemical Shifts in Solids and Liquids.

Mauri (1996)

10.1063/1.465574

"Ab initio" liquid water

K. Laasonen (1993)

10.1103/PhysRevLett.76.2934

New high-pressure phase of ice.

Benôıt (1996)

10.1080/001075197182450

The virtual matter laboratory

M. Gillan (1997)

10.1103/PHYSREVLETT.88.176401

Anharmonic Raman spectra in high-pressure ice from ab initio simulations.

A. Putrino (2002)

10.1103/RevModPhys.64.1045

Iterative minimization techniques for ab initio total energy calculations: molecular dynamics and co

M. Payne (1992)

10.1016/S0009-2614(98)01326-8

Ab initio centroid molecular dynamics: a fully quantum method for condensed-phase dynamics simulations

M. Pavese (1999)

10.1103/PHYSREVLETT.80.5145

Identification of Raman defect lines as signatures of ring structures in vitreous silica

A. Pasquarello (1998)