cookbook.md

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The OpenMM Cookbook

Getting Started

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notebooks/cookbook/first_simulation.ipynb

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Simulation Protocols

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notebooks/cookbook/Changing Temperature and Pressure notebooks/cookbook/Saving Systems to XML Files notebooks/cookbook/Merging Molecules notebooks/cookbook/Adding Hydrogens to Nonstandard Molecules :::

Restraints, Constraints, and External Forces

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glob: True caption: Restraints, Constraints, and External Forces

notebooks/cookbook/Applying a Constant External Force notebooks/cookbook/Constraining Atom Positions notebooks/cookbook/Restraining Atom Positions notebooks/cookbook/Restraining Dihedrals :::

Analysis and System Inspection

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glob: True caption: Analysis and System Inspection

notebooks/cookbook/Analyzing Energy Contributions notebooks/cookbook/Querying Charges and Other Parameters :::

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