Part I: The OpenMM Application Layer

• 2. Getting Started
  • 2.1. Introduction
  • 2.2. Installing OpenMM
• 3. Running Simulations
  • 3.1. A First Example
  • 3.2. Using AMBER Files
  • 3.3. Using Gromacs Files
  • 3.4. Using CHARMM Files
  • 3.5. The OpenMM-Setup Application
  • 3.6. Simulation Parameters
    • 3.6.1. Platforms
    • 3.6.2. Force Fields
    • 3.6.3. Small molecule parameters
    • 3.6.4. AMBER Implicit Solvent
    • 3.6.5. Nonbonded Interactions
    • 3.6.6. Constraints
    • 3.6.7. Heavy Hydrogens
    • 3.6.8. Integrators
    • 3.6.9. Temperature Coupling
    • 3.6.10. Pressure Coupling
    • 3.6.11. Energy Minimization
    • 3.6.12. Removing Center of Mass Motion
    • 3.6.13. Writing Trajectories
    • 3.6.14. Recording Other Data
    • 3.6.15. Saving Simulation Progress and Results
    • 3.6.16. Enhanced Sampling Methods
• 4. Model Building and Editing
  • 4.1. Adding Hydrogens
  • 4.2. Adding Solvent
  • 4.3. Adding a Membrane
  • 4.4. Adding or Removing Extra Particles
  • 4.5. Removing Water
  • 4.6. Saving The Results
• 5. Advanced Simulation Examples
  • 5.1. Simulated Annealing
  • 5.2. Applying an External Force to Particles: a Spherical Container
  • 5.3. Extracting and Reporting Forces (and other data)
  • 5.4. Computing Energies
• 6. Add-On Packages
  • 6.1. OpenMM-Torch
  • 6.2. OpenMM-ML
  • 6.3. OpenMMTools
  • 6.4. openmmforcefields
  • 6.5. OpenMM-PLUMED
• 7. Creating Force Fields
  • 7.1. Basic Concepts
    • 7.1.1. Atom Types and Atom Classes
    • 7.1.2. Residue Templates
    • 7.1.3. Forces
  • 7.2. Writing the XML File
    • 7.2.1. <AtomTypes>
    • 7.2.2. <Residues>
    • 7.2.3. <Patches>
    • 7.2.4. Missing residue templates
    • 7.2.5. <HarmonicBondForce>
    • 7.2.6. <HarmonicAngleForce>
    • 7.2.7. <PeriodicTorsionForce>
    • 7.2.8. <RBTorsionForce>
    • 7.2.9. <CMAPTorsionForce>
    • 7.2.10. <NonbondedForce>
    • 7.2.11. <GBSAOBCForce>
    • 7.2.12. <CustomBondForce>
    • 7.2.13. <CustomAngleForce>
    • 7.2.14. <CustomTorsionForce>
    • 7.2.15. <CustomNonbondedForce>
    • 7.2.16. <CustomGBForce>
    • 7.2.17. <CustomHbondForce>
    • 7.2.18. <CustomManyParticleForce>
    • 7.2.19. <LennardJonesForce>
    • 7.2.20. Writing Custom Expressions
    • 7.2.21. Tabulated Functions
    • 7.2.22. Residue Template Parameters
    • 7.2.23. Including Other Files
  • 7.3. Using Multiple Files
  • 7.4. Extending ForceField
    • 7.4.1. Adding new force types
    • 7.4.2. Adding residue template generators