OpenMM Users Manual and Theory Guide

Portions copyright (c) 2008-2014 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:

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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.

• 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 on Mac OS X
  • 3.2. Installing on Linux
  • 3.3. 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
• 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. <HarmonicBondForce>
    • 7.2.4. <HarmonicAngleForce>
    • 7.2.5. <PeriodicTorsionForce>
    • 7.2.6. <RBTorsionForce>
    • 7.2.7. <CMAPTorsionForce>
    • 7.2.8. <NonbondedForce>
    • 7.2.9. <GBSAOBCForce>
    • 7.2.10. <CustomBondForce>
    • 7.2.11. <CustomAngleForce>
    • 7.2.12. <CustomTorsionForce>
    • 7.2.13. <CustomNonbondedForce>
    • 7.2.14. <CustomGBForce>
    • 7.2.15. <CustomManyParticleForce>
    • 7.2.16. Writing Custom Expressions
    • 7.2.17. TabulatedFunctions
  • 7.3. Using Multiple Files
  • 7.4. Extending ForceField
• 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
• 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
• 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. AndersenThermostat
  • 19.9. MonteCarloBarostat
  • 19.10. MonteCarloAnisotropicBarostat
  • 19.11. MonteCarloMembraneBarostat
  • 19.12. CMMotionRemover
• 20. Custom Forces
  • 20.1. CustomBondForce
  • 20.2. CustomAngleForce
  • 20.3. CustomTorsionForce
  • 20.4. CustomNonbondedForce
  • 20.5. CustomExternalForce
  • 20.6. CustomCompoundBondForce
  • 20.7. CustomManyParticleForce
  • 20.8. CustomGBForce
  • 20.9. CustomHbondForce
  • 20.10. Writing Custom Expressions
• 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. LocalEnergyMinimizer
  • 22.2. XMLSerializer
  • 22.3. Force Groups
  • 22.4. Virtual Sites
• 23. Bibliography