OpenMM Users Manual and Theory Guide

• 1. Introduction
  • 1.1. Online Resources
  • 1.2. Referencing OpenMM
  • 1.3. Acknowledgments
• 2. The OpenMM Application Layer: Introduction
• 3. Installing OpenMM
  • 3.1. Installing with Conda
  • 3.2. Installing on Mac OS X
  • 3.3. Installing on Linux
  • 3.4. Installing on Windows
• 4. Running Simulations
  • 4.1. A First Example
  • 4.2. Using AMBER Files
  • 4.3. Using Gromacs Files
  • 4.4. Using CHARMM Files
  • 4.5. The Script Builder Application
  • 4.6. Simulation Parameters
    • 4.6.1. Platforms
    • 4.6.2. Force Fields
    • 4.6.3. AMBER Implicit Solvent
    • 4.6.4. Nonbonded Interactions
    • 4.6.5. Constraints
    • 4.6.6. Heavy Hydrogens
    • 4.6.7. Integrators
    • 4.6.8. Temperature Coupling
    • 4.6.9. Pressure Coupling
    • 4.6.10. Energy Minimization
    • 4.6.11. Removing Center of Mass Motion
    • 4.6.12. Writing Trajectories
    • 4.6.13. Recording Other Data
    • 4.6.14. Saving Simulation Progress and Results
• 5. Model Building and Editing
  • 5.1. Adding Hydrogens
  • 5.2. Adding Solvent
  • 5.3. Adding or Removing Extra Particles
  • 5.4. Removing Water
  • 5.5. Saving The Results
• 6. Advanced Simulation Examples
  • 6.1. Simulated Annealing
  • 6.2. Applying an External Force to Particles: a Spherical Container
  • 6.3. Extracting and Reporting Forces (and other data)
  • 6.4. Computing Energies
• 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. Writing Custom Expressions
    • 7.2.20. Tabulated Functions
    • 7.2.21. Residue Template Parameters
  • 7.3. Using Multiple Files
  • 7.4. Extending ForceField
    • 7.4.1. Adding new force types
    • 7.4.2. Adding residue template generators
• 8. The OpenMM Library: 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. Prerequisites
    • 9.1.1. Get a C++ compiler
    • 9.1.2. Install CMake
    • 9.1.3. Get the OpenMM source code
    • 9.1.4. Other Required Software
  • 9.2. Step 1: Configure with CMake
    • 9.2.1. Build and source directories
    • 9.2.2. Starting CMake
  • 9.3. Step 2: Generate Build Files with CMake
    • 9.3.1. Windows
    • 9.3.2. Mac and Linux
  • 9.4. Step 3: Build OpenMM
    • 9.4.1. Windows
    • 9.4.2. Mac and Linux
  • 9.5. Step 4: Install OpenMM
    • 9.5.1. Windows
    • 9.5.2. Mac and Linux
  • 9.6. Step 5: Install the Python API
    • 9.6.1. Windows
    • 9.6.2. Mac and Linux
  • 9.7. Step 6: Test your build
    • 9.7.1. Windows
    • 9.7.2. Mac and Linux
  • 9.8. Building the Documentation (Optional)
    • 9.8.1. User Guide and Developer Guide
    • 9.8.2. Python and C++ API Documentation
• 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. CPU Platform
  • 11.4. 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. Installing the Python API
    • 12.3.2. Mapping from the C++ API to the Python API
    • 12.3.3. Mechanics of using the Python API
    • 12.3.4. 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. TINKER-OpenMM
    • 15.2.1. Building TINKER-OpenMM (Linux)
    • 15.2.2. Using TINKER-OpenMM
  • 15.3. OpenMM AMOEBA Validation
• 16. Ring Polymer Molecular Dynamics (RPMD) Plugin
• 17. Drude Plugin
• 18. The Theory Behind OpenMM: Introduction
  • 18.1. Overview
  • 18.2. Units
• 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
  • 19.7. 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. CMMotionRemover
• 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. Writing Custom Expressions
  • 20.12. Parameter Derivatives
• 21. Integrators
  • 21.1. VerletIntegrator
  • 21.2. LangevinIntegator
  • 21.3. BrownianIntegrator
  • 21.4. VariableVerletIntegrator
  • 21.5. VariableLangevinIntegrator
  • 21.6. 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) 2008-2016 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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