iPHASimulator v2

Build PHA oligomers, prepare molecular simulations, and measure their structure and contacts. iPHASimulator is organised around practical notebooks with reusable Python helpers for polyhydroxyalkanoates (PHAs).

New here? Follow installation, then the P3HB_4 quick-start. For existing MD trajectories, start with trajectory preprocessing or enzyme–PHA contacts.

Workflow overview

Numbered boxes correspond to the tutorial notebooks; dashed outlines indicate optional routes or planned extensions. See the notebook catalogue for prerequisites and run order.

Choose your workflow

Start with	Follow	Result
A monomer code or 3-hydroxy-acid SMILES	Polymer design	An RDKit oligomer with a defined repeat count
A small oligomer structure	GAFF2 parameterisation	AMBER topology, coordinates and parameter logs
AMBER parameters	OpenMM / GROMACS preparation	Engine-specific inputs and run folders
Prepared simulation inputs	HPC execution	A reviewed execution plan and SLURM script
Completed MD outputs	Preprocessing → analysis	Processed trajectories, plots and tables
A candidate enzyme–PHA pair	Docking preparation	Inputs and records for a manual docking workflow

The teaching notebooks in notebooks/ cover construction, parameter preparation, simulation setup and selected analysis examples. Research analysis in src/md_simulation_scripts/ requires existing trajectories and system-specific paths; it is separate from the teaching sequence. Read the notebook catalogue for prerequisites and run order. Documentation builds do not execute notebooks.

The naming distinguishes the monomer (3HB), polymer (P3HB), and a chain with four repeats (P3HB_4). The quick-start explains construction, validation and export with that small example.

Start here

• Installation
  • 1. Get the repository
  • 2. Create a Python environment
  • 3. Add the tools for your workflow
  • 4. Check the installation
  • 5. Open a notebook
• Quick-start: construct, validate and export P3HB_4
  • 1. Construct the oligomer
  • 2. Validate the structure
  • 3. Export PDB and SDF
  • 4. Inspect the output
• Current capabilities and limitations
  • Validation and remaining limits
  • Teaching and research material

Workflow tutorials

• Polymer design
  • 1. Choose one design mode
  • 2. Validate and export
  • 3. If you use the AmberTools database route
• GAFF2 parameterisation
  • 1. Check prerequisites and choose paths
  • 2. Select the charge model deliberately
  • 3. Review the outputs
• OpenMM and GROMACS preparation
  • OpenMM: AMBER topology route
  • GROMACS with CHARMM-GUI inputs
  • GROMACS from GAFF2/AMBER files (conversion helpers)
  • Optional 06C: conditions and generated files
• Optional enzyme–PHA in water with OpenMM (06C)
  • Inputs, preparation and hand-off
  • Final 06B–06C conditions
  • Restart and analysis formats
  • Validation scope
• HPC execution
  • 1. Review the configuration
  • 2. Print a plan and generate a script
  • 3. Monitor and restart
  • Prepared 06A/06B/06C folders
• Trajectory preprocessing
  • 1. Choose exactly the intended trajectory
  • 2. Plan preprocessing
  • 3. Produce and inspect processed coordinates
• Standalone enzyme–PHA trajectory preparation
  • Parameterisation provenance
  • Automatic preparation notebook
  • 1. Prepare a new simulation’s analysis folder
  • 2. Edit instrcution.txt
  • 3. Check and run
  • 4. Analyse the full trajectory; view the reduced one
• Analysis
  • Enzyme–PHA distances and contacts
  • Basic polymer structure
  • Enzyme/polymer stability diagnostics
• Docking preparation
  • 1. Choose the polymer structure
  • 2. Prepare and inspect the PDB
  • 3. Prepare the enzyme separately
  • 4. Record the manual docking job
• Notebook catalogue
  • Construction and design
  • Parameterisation and simulation
  • Execution and analysis
  • Workflow order

Reference and contributing

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

Source: MMLabCodes/iPHAsimulatorV2. The capabilities documented here are specific to this repository.