Part III: The Theory Behind OpenMM

• 17. Introduction
  • 17.1. Overview
  • 17.2. Units
  • 17.3. Physical Constants
• 18. Standard Forces
  • 18.1. HarmonicBondForce
  • 18.2. HarmonicAngleForce
  • 18.3. PeriodicTorsionForce
  • 18.4. RBTorsionForce
  • 18.5. CMAPTorsionForce
  • 18.6. NonbondedForce
    • 18.6.1. Lennard-Jones Interaction
    • 18.6.2. Coulomb Interaction Without Cutoff
    • 18.6.3. Coulomb Interaction With Cutoff
    • 18.6.4. Coulomb Interaction With Ewald Summation
    • 18.6.5. Coulomb Interaction With Particle Mesh Ewald
    • 18.6.6. Lennard-Jones Interaction With Particle Mesh Ewald
  • 18.7. GBSAOBCForce
    • 18.7.1. Generalized Born Term
    • 18.7.2. Surface Area Term
  • 18.8. GayBerneForce
  • 18.9. AndersenThermostat
  • 18.10. MonteCarloBarostat
  • 18.11. MonteCarloAnisotropicBarostat
  • 18.12. MonteCarloMembraneBarostat
  • 18.13. MonteCarloFlexibleBarostat
  • 18.14. CMMotionRemover
  • 18.15. RMSDForce
• 19. Custom Forces
  • 19.1. CustomBondForce
  • 19.2. CustomAngleForce
  • 19.3. CustomTorsionForce
  • 19.4. CustomNonbondedForce
  • 19.5. CustomExternalForce
  • 19.6. CustomCompoundBondForce
  • 19.7. CustomCentroidBondForce
  • 19.8. CustomManyParticleForce
  • 19.9. CustomGBForce
  • 19.10. CustomHbondForce
  • 19.11. CustomCVForce
  • 19.12. Writing Custom Expressions
  • 19.13. Setting Parameters
  • 19.14. Parameter Derivatives
• 20. Integrators
  • 20.1. VerletIntegrator
  • 20.2. LangevinIntegator
  • 20.3. LangevinMiddleIntegrator
  • 20.4. NoseHooverIntegrator
  • 20.5. BrownianIntegrator
  • 20.6. VariableVerletIntegrator
  • 20.7. VariableLangevinIntegrator
  • 20.8. CustomIntegrator
• 21. Other Features
  • 21.1. Periodic Boundary Conditions
  • 21.2. LocalEnergyMinimizer
  • 21.3. XMLSerializer
  • 21.4. Force Groups
  • 21.5. Virtual Sites
  • 21.6. Random Numbers with Stochastic Integrators and Forces