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)
  • 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. CMMotionRemover
    • 18.14. 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

Permission is hereby granted, free of charge, to any person obtaining a copy of this document (the “Document”), to deal in the Document without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Document, and to permit persons to whom the Document is furnished to do so, subject to the following conditions:

This copyright and permission notice shall be included in all copies or substantial portions of the Document.

THE DOCUMENT IS PROVIDED “AS IS”, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE DOCUMENT OR THE USE OR OTHER DEALINGS IN THE DOCUMENT.