OpenMM Users Manual and Theory GuideΒΆ
Portions copyright (c) 2008-2014 Stanford University and the Authors
Contributors: Kyle Beauchamp, Christopher Bruns, Peter Eastman, Mark Friedrichs, Joy P. Ku, Vijay Pande, Randy Radmer, Michael Sherman, Tom Markland
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.
- 1. Introduction
- 2. The OpenMM Application Layer: Introduction
- 3. Installing OpenMM
- 4. Running Simulations
- 4.1. A First Example
- 4.2. Using AMBER Files
- 4.3. Using Gromacs Files
- 4.4. The Script Builder Application
- 4.5. Simulation Parameters
- 4.5.1. Platforms
- 4.5.2. Force Fields
- 4.5.3. AMBER Implicit Solvent
- 4.5.4. Nonbonded Interactions
- 4.5.5. Constraints
- 4.5.6. Heavy Hydrogens
- 4.5.7. Integrators
- 4.5.8. Temperature Coupling
- 4.5.9. Pressure Coupling
- 4.5.10. Energy Minimization
- 4.5.11. Removing Center of Mass Motion
- 4.5.12. Writing Trajectories
- 4.5.13. Recording Other Data
- 5. Model Building and Editing
- 6. Advanced Simulation Examples
- 7. Creating Force Fields
- 7.1. Basic Concepts
- 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. Writing Custom Expressions
- 7.2.16. TabulatedFunctions
- 7.3. Using Multiple Files
- 7.4. Extending ForceField
- 8. The OpenMM Library: Introduction
- 9. Compiling OpenMM from Source Code
- 10. OpenMM Tutorials
- 11. Platform-Specific Properties
- 12. Using OpenMM with Software Written in Languages Other than C++
- 13. Examples of OpenMM Integration
- 14. Testing and Validation of OpenMM
- 15. AMOEBA Plugin
- 16. Ring Polymer Molecular Dynamics (RPMD) Plugin
- 17. Drude Plugin
- 18. The Theory Behind OpenMM: Introduction
- 19. Standard Forces
- 20. Custom Forces
- 21. Integrators
- 22. Other Features
- 23. Bibliography