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Start here

  • Installation
  • Quick-start: construct, validate and export P3HB_4
  • Current capabilities and limitations

Workflow tutorials

  • Polymer design
  • GAFF2 parameterisation
  • OpenMM and GROMACS preparation
  • Optional enzyme–PHA in water with OpenMM (06C)
  • HPC execution
  • Trajectory preprocessing
  • Standalone enzyme–PHA trajectory preparation
  • Analysis
  • Docking preparation
  • Notebook catalogue

Reference and contributing

  • Python API reference
  • PHA–enzyme distance and contact workflow
  • iPHASimulator v2 Design
  • Repository README
  • Edit, preview and publish documentation
iPHASimulator v2
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