Part III: The Theory Behind OpenMM

• 18. Introduction
  • 18.1. Overview
  • 18.2. Units
  • 18.3. Physical Constants
• 19. Standard Forces
  • 19.1. HarmonicBondForce
  • 19.2. HarmonicAngleForce
  • 19.3. PeriodicTorsionForce
  • 19.4. RBTorsionForce
  • 19.5. CMAPTorsionForce
  • 19.6. NonbondedForce
    • 19.6.1. Lennard-Jones Interaction
    • 19.6.2. Coulomb Interaction Without Cutoff
    • 19.6.3. Coulomb Interaction With Cutoff
    • 19.6.4. Coulomb Interaction With Ewald Summation
    • 19.6.5. Coulomb Interaction With Particle Mesh Ewald
    • 19.6.6. Lennard-Jones Interaction With Particle Mesh Ewald
  • 19.7. GBSAOBCForce
    • 19.7.1. Generalized Born Term
    • 19.7.2. Surface Area Term
  • 19.8. GayBerneForce
  • 19.9. AndersenThermostat
  • 19.10. MonteCarloBarostat
  • 19.11. MonteCarloAnisotropicBarostat
  • 19.12. MonteCarloMembraneBarostat
  • 19.13. MonteCarloFlexibleBarostat
  • 19.14. CMMotionRemover
  • 19.15. RMSDForce
• 20. Custom Forces
  • 20.1. CustomBondForce
  • 20.2. CustomAngleForce
  • 20.3. CustomTorsionForce
  • 20.4. CustomNonbondedForce
  • 20.5. CustomExternalForce
  • 20.6. CustomCompoundBondForce
  • 20.7. CustomCentroidBondForce
  • 20.8. CustomManyParticleForce
  • 20.9. CustomGBForce
  • 20.10. CustomHbondForce
  • 20.11. CustomCVForce
  • 20.12. ATMForce
  • 20.13. Writing Custom Expressions
  • 20.14. Setting Parameters
  • 20.15. Parameter Derivatives
• 21. Integrators
  • 21.1. VerletIntegrator
  • 21.2. LangevinIntegator
  • 21.3. LangevinMiddleIntegrator
  • 21.4. NoseHooverIntegrator
  • 21.5. BrownianIntegrator
  • 21.6. VariableVerletIntegrator
  • 21.7. VariableLangevinIntegrator
  • 21.8. CustomIntegrator
• 22. Other Features
  • 22.1. Periodic Boundary Conditions
  • 22.2. LocalEnergyMinimizer
  • 22.3. XMLSerializer
  • 22.4. Force Groups
  • 22.5. Virtual Sites
  • 22.6. Random Numbers with Stochastic Integrators and Forces