Notebook catalogue

The original notebooks remain in the repository. Download one for local use, or view its existing contents on GitHub. Documentation builds never execute notebook cells, simulations, shell commands in notebooks, or stored outputs. The site links/downloads the source files rather than rendering them through an execution engine.

Install the relevant dependencies, start jupyter lab from the repository root, and choose your environment’s kernel. Review paths, selections, run switches and outputs before executing cells. Stored output is an illustration, not evidence that your inputs are valid. See capabilities and limits. 05A currently has RUN_GAFF2 = True. 10 executes selected-system preparation, solvation and minimisation and can submit with sbatch. Review those cells before Run All; this is different from 06A/06C’s default-off engine flags.

Construction and design

Notebook	Download	Status / prerequisites
Build a PHA oligomer	01_build_pha_oligomer.ipynb	RDKit; no MD dependencies
Design a custom PHA	02_design_custom_pha.ipynb	RDKit; no MD dependencies
Validate structures	03_validate_structures.ipynb	RDKit; no MD dependencies
Export structures	04_export_structures.ipynb	RDKit; no MD dependencies

Parameterisation and simulation

Notebook	Download	Status / prerequisites
Amber/GAFF2 parameters	05A_amber_gaff2_parameters.ipynb	AmberTools ≥23 for default ABCG2; exported SDF from 04
CHARMM/CGenFF parameters	05B_charmm_cgenff_parameters.ipynb	Manual CHARMM-GUI step; checks run on the example dataset by default
PHA (GAFF2) in water, GROMACS	06A_gaff2_gromacs_pha_in_water.ipynb	Polymer benchmark method; ParmEd + GROMACS; run flags off by default
PHA (CGenFF) + enzyme in water, GROMACS	06B_cgenff_gromacs_pha_enzyme_in_water.ipynb	Docked complex PDB (notebook 11); CHARMM-GUI Solution Builder download (default: the example dataset examples/data/charmm_gui_ANC55_P3HB4/); GROMACS optional
Optional: PHA (GAFF2) + enzyme in water, OpenMM	06C_optional_gaff2_openmm_pha_enzyme_in_water.ipynb	Docked complex PDB (notebook 11); tleap + OpenMM; a different force-field setup from 06B; run flags off by default
Optional: quick check of 05A parameters, OpenMM	05A_quick_check_openmm.ipynb	05A GAFF2 files in OpenMM without water; not a physical result; run flag off by default

Execution and analysis

For enzyme–PHA trajectory preparation, use the standalone Bash templates; the superseded GK13 preparation notebook is no longer needed.

Notebook	Download	Status / prerequisites
HPC execution	07_hpc_execution.ipynb	Prepared 06A/06B/06C folder; edit cluster/environment settings
Trajectory preprocessing	08_trajectory_preprocessing.ipynb	Requires GROMACS and MD inputs
Solvated polymer analysis	09_solvated_polymer_analysis.ipynb	MDTraj notebook workflow
Polymer benchmark batch	10_polymer_benchmark_batch.ipynb	Six-system GAFF2/GROMACS benchmark; external tools and output paths required
Enzyme docking setup	11_enzyme_docking_setup.ipynb	Manual; exports the polymer only from examples/output/benchmark/<SYSTEM>/ after a whole-molecule check; benchmark structure/topology required
Enzyme–polymer analysis	12_enzyme_polymer_analysis.ipynb	Energy and RMSD diagnostics; system-specific inputs
PHA–enzyme contacts	enzyme_contacts.ipynb	Reusable, validated preview; matching TPR/XTC required

Research analysis lives separately under src/md_simulation_scripts/: enzyme contacts, enzyme–PHA stability and APO inspection use existing simulation data. These are not additional steps in the teaching sequence and do not provide MD input files.

Workflow order

The notebooks are workflow modules, not a 01→12 sequence. Notebooks 01–04 build the PHA; then choose a route and use 07 for execution guidance:

• PHA alone in water: 05A → 06A

• Enzyme–PHA in water (the method used for the project’s research simulations): 05B → 06B

• Optional enzyme–PHA alternative with OpenMM: 05A → 06C

• Optional quick check of 05A parameters: 05A → 05A_quick_check_openmm (outside the main workflows)

Both enzyme workflows need a docked enzyme–PHA complex PDB first (docking preparation: notebook 11, then manual HADDOCK). For enzyme contacts, use the original periodic coordinates rather than an independently fitted trajectory with an untransformed box.

Use 08 → 09 for polymer trajectory preprocessing and Rg/end-to-end/SASA; 10 launches the six-system polymer benchmark; 11 exports its polymer frame for manual docking; 12 reads a completed GROMACS enzyme–PHA run. These are separate modules. 06C DCD/PDB output does not plug directly into the GROMACS TPR/XTC/EDR cells in 08/12. See 06C conditions and run-file checks.

The notebook guide is retained in the repository.