Forcefield-Based Simulations
Contents
Release 97.2, May 1998
Table of Contents
1. Introduction
Who should use this book
What can simulation engines do?
Energy minimization
Molecular dynamics
Other forcefield-based calculations
What are forcefields and simulation engines?
Using this guide
Additional information
Typographical conventions
2. Forcefields
The potential energy surface
Empirical fit to the potential energy surface
The forcefield
The energy expression
Forcefields supported by MSI forcefield engines
Main types of forcefields
Advantages of having several forcefields
Primary uses of each MSI forcefield
Second-generation forcefields accurate for many properties
CFF91, PCFF, CFF, COMPASS--consistent forcefields
Functional form
CFF91 forcefield
CFF forcefield
PCFF forcefield for polymers and other materials
COMPASS forcefield for polymers and other materials
MMFF93, the Merck molecular forcefield
Rule-based forcefields broadly applicable to the periodic table
ESFF, extensible systematic forcefield
Derivation
Functional form
Nonbond energy
ESFF atom types
UFF, universal forcefield
Dreiding forcefield
Classical forcefields
AMBER forcefield
Standard AMBER forcefield
Homans' carbohydrate forcefield
CHARMm forcefield
CVFF, consistent valence forcefield
Functional form
CVFF atom types
Special-purpose forcefields
Glass forcefield
MSXX forcefield for polyvinylidene fluoride
Zeolite forcefields
Forcefields for sorption on zeolites
Forcefields for Cerius2·Morphology module
Archived and untested forcefields
3. Preparing the Energy Expression and the Model
Using forcefields
Selecting forcefields
Assigning forcefield atom types and charges
What are atom types in forcefields?
Assigning atom types to a model
Assigning charges
Parameter assignment
Determination of which parameters are used with which atom types
Atom type equivalences
Wildcard atom types in the parameter file
Automatic assignment of values for missing parameters
Manual parameter assignment
Notification of missing parameters
Obtaining new parameters
Editing a forcefield
Using alternative forms of energy terms
Removing terms from the energy expression
Scaling or editing any selected type of term
Alternative bond terms
Scaled torsion terms
Inversion terms
Nonbond functional form
Hydrogen bonds and hydrogen-bond terms
Bond-angle cross terms vs. Urey-Bradley terms
Applying constraints and restraints
When to use constraints/restraints
Fixed atom constraints
Template forcing, tethering, quartic droplet restraints, and consensus conformations
General internal-coordinate restraints
Distance and NOE restraints
Distance and angle constraints in dynamics simulations
Angle restraints
Torsion restraints
Inversion, out-of-plane, and chiral restraints
Plane and other geometrical constraints and restraints
Modeling periodic systems
Minimum-image model
Explicit-image model
Crystal simulations
Bonds across boundaries
Handling nonbond interactions
Combination rules for van der Waals terms
The dielectric constant and the Coulombic term
Nonbond cutoffs
Atom-based cutoffs and nonbond cutoff terms
Neighbor lists and buffer widths
Charge groups and group-based cutoffs
Double cutoffs
Tail corrections
Cell-based cutoffs
Cell multipole method
Ewald sums for periodic systems
Nonbond energies of periodic systems
Theory of Ewald technique
Accuracy of Ewald calculations
Ewald sum for models with 2D periodicity
4. Minimization
General minimization process
Specific minimization example
Line search
Minimization algorithms
Steepest descents
Conjugate gradient
Newton-Raphson methods
Iterative Newton-Raphson method
Variants of iterative Newton-Raphson method
Quasi-Newton-Raphson
Truncated Newton-Raphson
General methodology for minimization
Minimizations with MSI simulation engines
When to use different algorithms
Convergence criteria
Significance of minimum-energy structure
Energy and gradient calculation
Vibrational calculation
Application of minimization to vibrational theory
Vibrational frequencies
Transition states
Thermodynamics
General methodology for vibrational calculations
5. Molecular Dynamics
Integration algorithms
Introduction
Criteria of good integrators in molecular dynamics
Integrators in MSI simulation engines
Verlet leapfrog integrator
Verlet velocity integrator
ABM4 integrator
Runge-Kutta-4 integrator
The choice of timestep
Integration errors
Example 1--Two colliding hydrogen atoms
Example 2--Energy conservation of a harmonic oscillator
Statistical ensembles
NVE ensemble
NVT ensemble
NPT and NST ensembles
NPH and NSH ensembles
Equilibrium thermodynamic properties
Temperature
How temperature is calculated
How temperature is controlled
Direct velocity scaling
Berendsen method of temperature-bath coupling
Nosé and Nosé-Hoover dynamics
Andersen method
Pressure and stress
Units and sign conventions for pressure and stress
How pressure and stress are calculated
How pressure and stress are controlled
Berendsen method of pressure control
Andersen method of pressure control
Parrinello-Rahman method of pressure and stress control
Types of dynamics simulations
Quenched dynamics
Simulated annealing
Consensus dynamics
Impulse dynamics
Langevin dynamics
Stochastic boundary dynamics
Multibody order-N dynamics
Constraints during dynamics simulations
The SHAKE algorithm
The RATTLE algorithm
Dynamics trajectories
General methodology for dynamics calculations
Stages and duration of dynamics simulations
Dynamics with MSI simulation engines
Restarting a dynamics simulation
6. Free Energy
Relative free energy--theory and implementation
Finite difference thermodynamic integration (FDTI)
Relative free energy--methodology
Absolute free energy
Theory and implementation
Example: Fentanyl
Analysis of results
APPENDICES
A. References
B. Forcefield Terms and Atom Types
Forcefield term definitions
AMBER atom types
Standard AMBER forcefield
Homan's carbohydrate forcefield
CFF91 atom types
CHARMm atom types
COMPASS atom types
CVFF atom types
CVFF_aug atom types
ESFF atom types
PCFF--additional atom types
List of Figures
List of Tables
Index
Last updated January 8, 1998.
Copyright © 1997, 1998, Molecular Simulations, Inc. All rights reserved.
