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
      • 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
• Part II: The OpenMM Library
  • 8. Introduction
    • 8.1. What Is the OpenMM Library?
      • 8.1.1. How to get started
      • 8.1.2. License
    • 8.2. Design Principles
    • 8.3. Choice of Language
    • 8.4. Architectural Overview
    • 8.5. The OpenMM Public API
    • 8.6. The OpenMM Low Level API
    • 8.7. Platforms
  • 9. Compiling OpenMM from Source Code
    • 9.1. Compiling on Linux and Mac
      • 9.1.1. Prerequisites
      • 9.1.2. Step 1: Configure with CMake
      • 9.1.3. Step 2: Build
      • 9.1.4. Step 3: Test your build
      • 9.1.5. Step 3: Install
      • 9.1.6. Step 3: Install the Python API
    • 9.2. Compiling on Windows
      • 9.2.1. Prerequisites
      • 9.2.2. Step 1: Configure with CMake
      • 9.2.3. Step 2: Build and Install
      • 9.2.4. Step 3: Install the Python API
      • 9.2.5. Step 4: Test your build
    • 9.3. Building the Documentation (Optional)
    • 9.4. Using local build of OpenMM alongside conda tools that depend on it
      • 9.4.1. Step 1: Install your tools as usual
      • 9.4.2. Step 2: Remove conda openmm package
      • 9.4.3. Step 3: Install local build of openmm
  • 10. OpenMM Tutorials
    • 10.1. Example Files Overview
    • 10.2. Running Example Files
      • 10.2.1. Visual Studio
      • 10.2.2. Mac OS X/Linux
    • 10.3. HelloArgon Program
      • 10.3.1. Including OpenMM-defined functions
      • 10.3.2. Running a program on GPU platforms
      • 10.3.3. Running a simulation using the OpenMM public API
      • 10.3.4. Error handling for OpenMM
      • 10.3.5. Writing out PDB files
      • 10.3.6. HelloArgon output
    • 10.4. HelloSodiumChloride Program
      • 10.4.1. Simple molecular dynamics system
      • 10.4.2. Interface routines
    • 10.5. HelloEthane Program
  • 11. Platform-Specific Properties
    • 11.1. OpenCL Platform
    • 11.2. CUDA Platform
    • 11.3. HIP Platform
    • 11.4. CPU Platform
    • 11.5. Determinism
  • 12. Using OpenMM with Software Written in Languages Other than C++
    • 12.1. C API
      • 12.1.1. Mechanics of using the C API
      • 12.1.2. Mapping from the C++ API to the C API
      • 12.1.3. Exceptions
      • 12.1.4. OpenMM_Vec3 helper type
      • 12.1.5. Array helper types
    • 12.2. Fortran 95 API
      • 12.2.1. Mechanics of using the Fortran API
      • 12.2.2. Mapping from the C++ API to the Fortran API
      • 12.2.3. OpenMM_Vec3 helper type
      • 12.2.4. Array helper types
    • 12.3. Python API
      • 12.3.1. Mapping from the C++ API to the Python API
      • 12.3.2. Mechanics of using the Python API
      • 12.3.3. Units and dimensional analysis
  • 13. Examples of OpenMM Integration
    • 13.1. GROMACS
    • 13.2. TINKER-OpenMM
  • 14. Testing and Validation of OpenMM
    • 14.1. Description of Tests
      • 14.1.1. Unit tests
      • 14.1.2. System tests
      • 14.1.3. Direct comparisons between OpenMM and other programs
    • 14.2. Test Results
      • 14.2.1. Comparison to Reference Platform
      • 14.2.2. Energy Conservation
      • 14.2.3. Comparison to Gromacs
  • 15. AMOEBA Plugin
    • 15.1. OpenMM AMOEBA Supported Forces and Options
      • 15.1.1. Supported Forces and Options
      • 15.1.2. Supported Integrators
    • 15.2. OpenMM AMOEBA Validation
  • 16. Ring Polymer Molecular Dynamics (RPMD) Plugin
  • 17. Drude Plugin
• 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

• 23. 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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