This repository describes setting up and running host-guest binding free energy calculations on cyclodextrins using the SMIRNOFF99Frosst force field.

For information related to the setup and analysis of the calculations, please see:

• GitHub repository used to convert AMBER input files from GAFF force field to SMIRNOFF99Frosst.
• GitHub repository for setting up the attach-pull-release calculations using paprika version 0.0.3.
• GitHub repository for analyzing the simulations and generating the plots in this manuscript.
• GitHub repository for the Open Force Field group containing the toolkit and force field XML file.

Except when noted otherwise, the entirety of this repository is licensed under a CC BY 4.0 License (LICENSE.md), which allows reuse with attribution. Please attribute by linking to https://github.com/slochower/smirnoff-host-guest-manuscript.

Since CC BY is not ideal for code and data, certain repository components are also released under the CC0 1.0 public domain dedication (LICENSE-CC0.md). All files matched by the following glob patterns are dual licensed under CC BY 4.0 and CC0 1.0:

• *.sh
• *.py
• *.yml / *.yaml
• *.json
• *.bib
• *.tsv
• .gitignore

All other files are only available under CC BY 4.0, including:

• *.md
• *.html
• *.pdf
• *.docx

Except for the following files with different licenses:

• build/assets/anchors.js which is released under an MIT License

Please open an issue for any question related to licensing.