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Openmm users manual and theory guide

OpenMM Users Manual and Theory Guide Release September Website simtk org home openmm OpenMM Users Manual and Theory Guide Authors Kyle Beauchamp Christopher Bruns Peter Eastman Mark Friedrichs Joy P Ku Tom Markland Vijay Pande Randy Radmer Michael Sherman Copyright and Permission Notice Portions copyright c - 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 v Acknowledgments OpenMM software and all related activities such as this manual are funded by the Simbios National Center for Biomedical Computing through the National Institutes of Health Roadmap for Medical Research Grant U GM Information on the National Centers can be found at http nihroadmap nih gov bioinformatics Table of Contents ? INTRODUCTION ? ? Online Resources ? ? Referencing OpenMM ? ? INTRODUCTION TO THE OPENMM APPLICATION LAYER ? ? INSTALLING OPENMM ? ? Installing on Mac OS X ? ? Installing on Linux ? ? Installing on Windows ? ? RUNNING SIMULATIONS ? ? A First Example ? ? Using AMBER Files ? ? Using Gromacs Files ? ? The Script Builder Application ? ? Simulation Parameters ? ? Platforms ? ? Force Fields ? ? AMBER Implicit Solvent ? ? Nonbonded Interactions ? ? Constraints ? ? Heavy Hydrogens ? ? Integrators ? ? Temperature Coupling ? ? Pressure Coupling ? ? Energy Minimization ? ? Removing Center of Mass Motion ? ? Writing Trajectories ? ? Recording Other Data ? ? MODEL BUILDING AND EDITING ? ? Adding Hydrogens ? vii ? Adding Solvent ? ? Adding or Removing Extra Particles ? ? Removing Water ? ? Saving The Results ? ? ADVANCED SIMULATION EXAMPLES ? ? Simulated Annealing ? ? Applying an External Force to Particles a Spherical Container ? ? Extracting and Reporting Forces and other data ? ? Computing Energies ? ? CREATING FORCE FIELDS ? ? Basic Concepts ? ? Atom Types and Atom Classes ? ? Residue Templates ? ? Forces ? ? Writing the XML File ? ? ? ?