The OpenMM Cookbook

Getting Started

• First Simulation

Simulation Protocols

• Changing Temperature and Pressure
• Saving Systems to XML Files
• Merging Molecules in a Topology
• Adding Hydrogens to Nonstandard Molecules

Restraints, Constraints, and External Forces

• Applying a Fixed External Force
• Constraining Atom Positions
• Restraining Atom Positions
• Restraining Dihedrals

Analysis and System Inspection

• Analyzing Energy Contributions
• Computing Interaction Energies
• Querying and Modifying Charges and Other Parameters
• Reporting Minimization