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Handbook of Molecular Dynamics Potential Functions

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Handbook of Molecular Dynamics Potential Functions

John R. Lloyd
Mechanical and Astronautical Engineering Naval Postgraduate School

Tengfei Luo


This handbook is a result of research in identifying potential functions for use in molecular dynamic simulation. Potential functions by name have been listed and then cross-listed by the molecular systems that they have been used to simulate. We hope that this handbook will prove useful to others involved in performing molecular dynamic simulations. Research continues to be done to locate more potential functions and information about the systems that they can describe.

245 pages, © 2011

Tabla de Contenidos:

1. Introduction
1.1 Ab-initio Method
1.2 Classical Molecular Dynamics
1.3 Empirical Potential
1.3.1 Choosing the Right Potential Model
1.3.2 Determination of Potential Parameters
1.3.3 Transferability
1.4 Objective of This Book
Part I Two-Body Potentials
4th power — General Purpose Potential
AIREBO — Hydrocarbons
Berne–Pechukas — Ellipsoidal Gaussians
Beest–Kramer–Santen (BKS) — Silica and Aluminophosphate
Biswas–Hamann — Silicon Structural Energies
Born repulsive — Ionic Crystal
Born–Huggins–Mayer — NaCl-type Alkali Halides
Born–Mayer — Neutral Ground-State Atoms with Z = 2 to Z = 105
Born–Pauling — Ionic Compounds
Brenner —
Brenner II (REBO) — Hydrocarbons
Buckingham — Various Elements and Compounds
Chelikowsky — Formation of C60 Clusters
Coulombic — Any Charged Atom
Diep–Johnson — H2–H2 Interaction
Dipole — Particles with Charge and/or Point Dipole Moment
Dissipative particle dynamics (DPD) — Large Scale Soft, Repulsive Spheres
Embedded-Atom Method (EAM) — Metals and Semiconductors
Finite Extensible Nonlinear Elastic (FENE) — Bead-Spring Linear Polymer Melt
Fermi–Dirac — General Purpose Potential
Feuston–Garofalini — H2O–Silicate Reactive System
Gay–Berne — Aspherical Molecules
Hybrid Extended Rydberg — Alkali Metal Trimers
Harmonic — General Purpose Potential
Inverted Gaussian — General Purpose Potential
Kaxiras-Pandey, Murrell–Mottram — 2-, 3-Body Potentials for Si
Lennard-Jones —
Ag Film Growth on Cu
Hydrogen in Carbon Nanotubes
Inert Monatomic Molecules
Inert Gas–Hydrogen Halide
Murrell–Carter–Farantos–Huxley–Varandas (MCFHV) —
2- and 3-Body LiFH Potential
Mittal–Chaplot — ZrW2O8
Modified Stillinger–Weber — O (Oxygen) Defects in Silicon Crystal
Morse —
Cubic Metals
Polynomial — General Purpose Potential
Quartic — Breakable Bond Interaction
Rector–Swol — General Purpose Bond Potential
Rydberg (Extended) — CO and H2
Silvera–Goldman — H2 and D2 in Solid and Gas Phases
Silvera–Goldman/Deep–Johnson — Hydrogen in Carbon SWNT
Squared Harmonic — Molecular System
Stillinger–Weber —
Silicon Solid and Liquid
Supercooled Liquid Silicon
Tang–Toennies — van der Waals Potential Model
Tersoff —
Defect Properties in 3C–SiC
Structural Properties of Si
Modified Potential for Si
Tersoff–Brenner — Silicon and Carbon
Yamaguchi–Maruyama — Fullerene Formation
Yukawa — Particles that Exchange Massive Scalar Field
Zhu–Philpott — H2O on Platinum Solid Surface
Part II Three-Body Potentials
Axilrod–Teller — 3-Body van der Waals Type Interaction
Cosine Angular — General Purpose Potential
Squared Cosine Angle — General Purpose Potential
Exponential 3-Body — General Purpose Potential
Harmonic Angle — General Purpose Potential
Murrell–Mottram Angle — General Purpose Potential
Urey–Bradley Angle — General Purpose Potential
Part III Four-Body Potentials
Cosine Dihedral — General Purpose Potential
ESFF Dihedral — General Purpose Potential
Exponential Dihedral — General Purpose Potential
Guo–Thirumalai Dihedral — General Purpose Potential
Harmonic–Cosine Dihedral — General Purpose Potential
Harmonic Dihedral — General Purpose Potential
OPLS Dihedral — General Purpose Potential
Polynomial Dihedral — General Purpose Potential
Triple Cosine Dihedral — General Purpose Potential
Part IV Integrated Force Fields
AMBER — Proteins, Nucleic Acids, Organic Molecules
CFF — Organic Compounds, Polymers, Metals
CHARMM — Biological Systems
COMPASS — Organic/Inorganic Molecules, Polymers
DREIDING — Any Nonmetallic Main-Group Element
GROMACS — Biochemical Molecules and Polymers
ReaxFF — Reactive Systems
UFF — Any Material
Subject Index