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. 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. 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