├── .github └── workflows │ └── python-publish.yml ├── .gitignore ├── .readthedocs.yaml ├── .travis.yml ├── .vscode └── settings.json ├── FastMBAR ├── __init__.py ├── fastmbar.py ├── test_FastMBAR.py └── utils │ ├── analyzer.py │ └── fastmbartools.py ├── LICENSE ├── README.rst ├── docs ├── .gitignore ├── Makefile ├── requirements.txt └── source │ ├── API.rst │ ├── _static │ ├── logo.ai │ ├── logo.eps │ └── logo.png │ ├── butane_PMF.rst │ ├── conf.py │ ├── dialanine_PMF.rst │ ├── examples.rst │ ├── index.rst │ ├── installation.rst │ ├── references.rst │ └── usage.rst ├── energy_matrix.pdf ├── energy_matrix.png ├── examples ├── butane │ ├── .gitignore │ ├── data │ │ ├── Fig_1.png │ │ ├── Fig_2.png │ │ ├── PMF.png │ │ ├── butane.coor │ │ ├── butane.pdb │ │ ├── butane.psf │ │ ├── energy_matrix.png │ │ ├── par_all35_ethers.prm │ │ └── top_all35_ethers.rtf │ ├── output │ │ ├── .gitignore │ │ ├── PMF_fast_mbar.pdf │ │ ├── dihedral │ │ │ └── .gitignore │ │ ├── system.xml │ │ ├── theta0.csv │ │ └── traj │ │ │ └── .gitignore │ └── script │ │ ├── .gitignore │ │ ├── collect_dihedral.py │ │ ├── compute_pmf_with_analyzer.py │ │ ├── compute_pmf_with_fastmbar.py │ │ ├── compute_pmf_with_nflows.py │ │ ├── main.ipynb │ │ ├── make_system.py │ │ └── umbrella_sampling.py └── dialanine │ ├── .gitignore │ ├── data │ ├── Fig_1.png │ ├── Fig_2.png │ ├── PMF.png │ ├── dialanine.coor │ ├── dialanine.pdb │ ├── dialanine.psf │ ├── par_all36_prot.prm │ └── top_all36_prot.rtf │ ├── output │ ├── .gitignore │ ├── dialanine.coor │ ├── dialanine.pdb │ ├── dialanine.psf │ ├── system.xml │ └── traj │ │ └── .gitignore │ └── script │ ├── .gitignore │ ├── analyze_umbrella_dialanine.py │ ├── compute_pmf_fastmbar.py │ ├── main.ipynb │ ├── make_psf.inp │ ├── make_system.py │ ├── run_umbrella_dialanine.py │ ├── umbrella_sampling.py │ └── umbrella_sampling.spy └── pyproject.toml /.github/workflows/python-publish.yml: -------------------------------------------------------------------------------- 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