The OpenMM Cookbook¶

Simulation Protocols¶

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Changing Temperature and Pressure

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Saving Systems to XML Files

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Merging Molecules in a Topology

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Adding Hydrogens to Nonstandard Molecules

Restraints, Constraints, and External Forces¶

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Applying a Fixed External Force

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Constraining Atom Positions

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Restraining Atom Positions

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Restraining Dihedrals

Analysis and System Inspection¶

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Analyzing Energy Contributions

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Querying Charges and Other Parameters


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  • Changing Temperature and Pressure →

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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
  • Querying Charges and Other Parameters
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  • Python API reference
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