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