3. Reference Manual

• 3.1. Energy Function
  • 3.1.1. Non-bonded interactions
    • 3.1.1.1. Coulomb Interaction using Point charges
    • 3.1.1.2. Coulomb Interaction using Gaussian charges
    • 3.1.1.3. Coulomb Interaction using Slater charges
    • 3.1.1.4. Long range Coulomb interactions
    • 3.1.1.5. Polarization
    • 3.1.1.6. Induction correction
    • 3.1.1.7. Pauli Repulsion and London Dispersion
    • 3.1.1.8. Treatment of long range dispersion
    • 3.1.1.9. Combination Rules for Van der Waals Potentials
  • 3.1.2. Bonded interactions
    • 3.1.2.1. Harmonic potential
    • 3.1.2.2. Morse potential
    • 3.1.2.3. Wei-Hua potential
    • 3.1.2.4. Angle potential
    • 3.1.2.5. Angle potential for linear compounds
    • 3.1.2.6. Out-of-plane vibrations
    • 3.1.2.7. Torsion potential
    • 3.1.2.8. Proper dihedral
  • 3.1.3. Special potentials
  • 3.1.4. Virtual Sites
  • 3.1.5. Total energy
• 3.2. Force Field Training Algorithms
  • 3.2.1. MCMC
    • 3.2.1.1. Metropolis Criterion
    • 3.2.1.2. Multiple MCMC runs
  • 3.2.2. Genetic Algorithm
    • 3.2.2.1. Initialization
    • 3.2.2.2. Deviation from data
    • 3.2.2.3. Sorting
    • 3.2.2.4. Penalties
    • 3.2.2.5. Selection probabilities
    • 3.2.2.6. Rank
    • 3.2.2.7. Fitness
    • 3.2.2.8. Boltzmann
    • 3.2.2.9. Elitism
    • 3.2.2.10. Selection
    • 3.2.2.11. Crossover
    • 3.2.2.12. Mutation
    • 3.2.2.13. Termination
  • 3.2.3. HYBRID
• 3.3. Force field design
  • 3.3.1. Physical Background
  • 3.3.2. Determining atom types
  • 3.3.3. Determining partial charges
  • 3.3.4. Charge Equilibration with Shells or Virtual Sites
• 3.4. Force Field Training Targets
  • 3.4.1. Algorithm to compute energy components in ACT
  • 3.4.2. Monomer Energies and Forces
  • 3.4.3. Other Properties
• 3.5. Parameters for Force Field Training
• 3.6. Training Data
  • 3.6.1. Using existing data
  • 3.6.2. Alexandria Library
  • 3.6.3. Donchev data set
  • 3.6.4. Non-covalent interaction atlas
  • 3.6.5. ACT data
  • 3.6.6. Generating SAPT data
  • 3.6.7. Generating single molecule data
  • 3.6.8. Conversion to ACT molprop files