The OpenMM Cookbook

Getting Started

Getting Started

First Simulation

Simulation Protocols

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

Restraints, Constraints, and External Forces

Applying a Fixed External Force

Constraining Atom Positions

Restraining Atom Positions

Restraining Dihedrals

Analysis and System Inspection

Analysis and System Inspection

Analyzing Energy Contributions

Computing Interaction Energies

Querying and Modifying Charges and Other Parameters

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