Forcefield Based Simulations |

- Who should use this documentation
- 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
- 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
- MMFF94 and MMFF94s, the Merck molecular forcefield

- Rule-based forcefields broadly applicable to the periodic table
- ESFF, extensible systematic forcefield
- UFF, universal forcefield
- VALBOND
- Dreiding forcefield

- Classical forcefields
- AMBER forcefield
- CHARMm forcefield
- CVFF, consistent valence forcefield

- 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
- 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
- Automatic assignment of values for missing parameters
- Manual parameter assignment

- 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
- Cell multipole method
- Ewald sums for periodic systems

- General minimization process
- Specific minimization example
- Line search

- Minimization algorithms
- Steepest descents
- Conjugate gradient
- Newton-Raphson methods

- 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
- General methodology for vibrational calculations

- Integration algorithms
- Introduction
- Criteria of good integrators in molecular dynamics
- Integrators in MSI simulation engines

- 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

- Pressure and stress
- Units and sign conventions for pressure and stress
- How pressure and stress are calculated
- How pressure and stress are controlled

- 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

- 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

- 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

Last updated September 10, 1998.