OpenMM User’s Manual and Theory Guide

• 1. Introduction
  • 1.1. Online Resources
  • 1.2. Referencing OpenMM
  • 1.3. Acknowledgments

• 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
  • 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. Creating Force Fields
    • 6.1. Basic Concepts
    • 6.2. Writing the XML File
    • 6.3. Using Multiple Files
    • 6.4. Extending ForceField
• Part II: The OpenMM Library
  • 7. Introduction
    • 7.1. What Is the OpenMM Library?
    • 7.2. Design Principles
    • 7.3. Choice of Language
    • 7.4. Architectural Overview
    • 7.5. The OpenMM Public API
    • 7.6. The OpenMM Low Level API
    • 7.7. Platforms
  • 8. Compiling OpenMM from Source Code
    • 8.1. Compiling on Linux and Mac
    • 8.2. Compiling on Windows
    • 8.3. Building the Documentation (Optional)
    • 8.4. Using local build of OpenMM alongside conda tools that depend on it
  • 9. OpenMM Tutorials
    • 9.1. Example Files Overview
    • 9.2. Running Example Files
    • 9.3. HelloArgon Program
    • 9.4. HelloSodiumChloride Program
    • 9.5. HelloEthane Program
  • 10. Platform-Specific Properties
    • 10.1. OpenCL Platform
    • 10.2. CUDA Platform
    • 10.3. CPU Platform
    • 10.4. Determinism
  • 11. Using OpenMM with Software Written in Languages Other than C++
    • 11.1. C API
    • 11.2. Fortran 95 API
    • 11.3. Python API
  • 12. Examples of OpenMM Integration
    • 12.1. GROMACS
    • 12.2. TINKER-OpenMM
  • 13. Testing and Validation of OpenMM
    • 13.1. Description of Tests
    • 13.2. Test Results
  • 14. AMOEBA Plugin
    • 14.1. OpenMM AMOEBA Supported Forces and Options
    • 14.2. OpenMM AMOEBA Validation
  • 15. Ring Polymer Molecular Dynamics (RPMD) Plugin
  • 16. Drude Plugin
• 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
    • 18.7. GBSAOBCForce
    • 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

• 22. Bibliography

Portions copyright (c) 2008-2017 Stanford University and the Authors

Contributors: Kyle Beauchamp, Christopher Bruns, John Chodera, Peter Eastman, Mark Friedrichs, Joy P. Ku, Tom Markland, Vijay Pande, Randy Radmer, Michael Sherman, Jason Swails, Lee-Ping Wang

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