GO Workbench

Generate graphene oxide sheets with explicit connectivity and optional covalent functionalization.

Contents

• Getting started
• Usage and examples
• Data and files
• Methods and validation
• Documentation
• Citation
• Contributing
• License

Note

New parameters, charges and topologies are preliminary. See the validation status before using them in simulations.

Getting started

Requires Python 3.11 or later; the bundled quickstart uses Python 3.12. From the repository root:

uv sync --frozen
uv run python examples/quickstart/run_quickstart.py --output-dir work/quickstart

The example builds a small sheet, checks its connectivity and prepares Amber inputs using Python dependencies. Install AmberTools to compile a topology; later QM, docking and simulation steps use their respective external engines.

Quickstart and expected outputs · Installation details · Engine setup

Usage and examples

Build and functionalize a GO sheet with: 01_build_GO.py → 02_open_epoxides.py (optional) → 03_prepare_amber.py. Use prepare_fragment.py to prepare grafting reagents for reuse across loadings and random seeds.

To run the quickstart steps separately:

uv run python 01_build_GO.py --recipe examples/finite_GO.json --output work/finite_GO.json --pdb work/finite_GO.pdb --json
uv run python check_model.py --model work/finite_GO.json --json
uv run python 03_prepare_amber.py --model work/finite_GO.json --output-dir work/amber --radii mbondi2

Data and files

Output under work/quickstart/	Contents
finite_GO.json, finite_GO.pdb	Sheet connectivity and coordinates
amber/tleap.in, amber/GO_gaff2.frcmod	LEaP input and parameter modifications
amber/assigned_model.json, amber/library_audit.json	Atom-type and library assignments
amber/manifest.json, amber/normalized_libraries/	Input manifest and unit libraries

The command reference lists the build, functionalization, parameterization, docking and export scripts.

Methods and validation

The charge presets include the published GAFF2–AIM parameters, the current libraries and the HierGO/OPLS reference. Parameterization studies cover RESP development; experimental parameters are kept separate from the reference libraries.

VALIDATION.md lists completed regression benchmarks and parameterization work still in progress. COMPARISON.md compares methodologies against HierGO and GOPY. Original reference files are indexed in resources/reference/SOURCES.json; HierGO/OPLS tracks commit SHAs, file hashes, and upstream licenses in resources/reference/opls/PROVENANCE.json.

Graph checks establish connectivity and coordination. They do not establish electronic structure, parameter accuracy or equilibration. See the charge-derivation reference for the QM and ESP workflow.

Documentation

Topic index

• Installation & Environment Setup
• Scripts & Usage Workflow
• Generating a Graphene Oxide Sheet
• Construction Details
• Covalent Functionalization (Amino Acids, PEG, Peptides, Cyclodextrins)
• Amber Topologies, Periodicity, Docking & MM/GBSA
• Receptor Preparation and 3D Bounding Boxes
• AutoDock Vina & Empirical GNINA Docking
• Complex Assembly for MD & MM/GBSA
• Charge Derivation: Audits & Validation
• Local Execution & Slurm Integration
• Validation Status & Original Baselines
• Citation & License

Topic	Guide
First example	Quickstart
Commands and complete workflows	Command reference
Covalent functionalization	Fragments
Charge models and presets	Charge presets
External programs	Engine setup
Validation and limitations	Validation
Development plans and timings	Roadmap · Benchmarks

Trajectory alignment.

Citation

If you use this software or its parameter libraries, cite the archived release:

Alessandro Calza (2026). GO Workbench, version 0.1.0. DOI: 10.5281/zenodo.24119849.

Citation metadata: CITATION.cff.

BibTeX

@software{Calza2026GOWorkbench,
  author = {Alessandro Calza},
  title = {GO Workbench},
  version = {0.1.0},
  year = {2026},
  doi = {10.5281/zenodo.24119849},
  url = {https://github.com/CalzaAlessandro/go-surface-workbench}
}

Contributing

See CONTRIBUTING.md for setup and checks. Report problems or propose changes through GitHub Issues. Include the affected file or command and a short description.

License

This project is licensed under the Apache 2.0 License.