├── .gitignore ├── LICENSE ├── README.md ├── docs ├── .buildinfo ├── .nojekyll ├── Makefile ├── build │ ├── doctrees │ │ ├── environment.pickle │ │ ├── index.doctree │ │ └── sections │ │ │ ├── introduction.doctree │ │ │ └── models.doctree │ └── html │ │ ├── .buildinfo │ │ ├── .nojekyll │ │ ├── _modules │ │ ├── core │ │ │ ├── geometry.html │ │ │ ├── models.html │ │ │ └── system.html │ │ ├── index.html │ │ └── reporter │ │ │ └── sbm_reporter.html │ │ ├── _sources │ │ ├── index.rst.txt │ │ └── sections │ │ │ ├── introduction.rst.txt │ │ │ └── models.rst.txt │ │ ├── _static │ │ ├── alabaster.css │ │ ├── basic.css │ │ ├── custom.css │ │ ├── doctools.js │ │ ├── documentation_options.js │ │ ├── file.png │ │ ├── jquery-3.4.1.js │ │ ├── jquery.js │ │ ├── language_data.js │ │ ├── minus.png │ │ ├── plus.png │ │ ├── pygments.css │ │ ├── searchtools.js │ │ ├── underscore-1.3.1.js │ │ └── underscore.js │ │ ├── genindex.html │ │ ├── index.html │ │ ├── objects.inv │ │ ├── py-modindex.html │ │ ├── search.html │ │ ├── searchindex.js │ │ └── sections │ │ ├── introduction.html │ │ └── models.html ├── index.html └── source │ ├── conf.py │ ├── index.rst │ └── sections │ ├── introduction.rst │ └── models.rst ├── sbmOpenMM ├── __init__.py ├── core │ ├── __init__.py │ ├── geometry.py │ ├── models.py │ └── system.py ├── datasets │ ├── __init__.py │ ├── downloader.py │ └── foxp1_folding.py ├── parameters │ ├── __init__.py │ ├── amber.json │ ├── amber.py │ ├── ca_parameters.py │ └── oplsaa.py └── reporter │ ├── __init__.py │ └── sbm_reporter.py ├── setup.py └── tutorials ├── basic ├── 01-AlphaCarbon │ ├── coarseGrainedSBM.ipynb │ └── inputs │ │ ├── 1YPA_I.pdb │ │ └── 1YPA_I_CA.contacts ├── 02-AllAtom │ ├── allHeavyAtomSBM.ipynb │ └── inputs │ │ ├── 1YPA_I.pdb │ │ └── 1YPA_I_AA.contacts ├── 03-FoldingTemperature │ ├── foldingTemperature.ipynb │ └── inputs │ │ ├── 1YPA_I.pdb │ │ ├── 1YPA_I_CA.contacts │ │ ├── pywham_hc_better_estimate.xml │ │ ├── pywham_hc_rough_estimate.xml │ │ ├── pywham_iterative_01.xml │ │ ├── pywham_iterative_02.xml │ │ ├── pywham_iterative_03.xml │ │ ├── pywham_iterative_04.xml │ │ ├── pywham_iterative_05.xml │ │ ├── pywham_iterative_06.xml │ │ ├── pywham_iterative_07.xml │ │ ├── pywham_iterative_08.xml │ │ ├── pywham_iterative_09.xml │ │ └── pywham_iterative_10.xml ├── 04-FreeEnergySurface │ ├── freeEnergyProfile.ipynb │ └── inputs │ │ ├── 1YPA_I.pdb │ │ ├── 1YPA_I_CA.contacts │ │ ├── pywham_Qf_RMSD_free_energy.xml │ │ ├── pywham_Qf_free_energy.xml │ │ └── pywham_RMSD_free_energy.xml └── 05-MultiBasin │ ├── input │ ├── AK_close.pdb │ ├── AK_close_CA.contacts │ ├── AK_conformationalChange.webm │ ├── AK_open.pdb │ ├── AK_open_CA.contacts │ └── fe_wham.xml │ └── multiBasinModel.ipynb └── folding └── 01-FoxP1_equilibrium_folding ├── 01-Production.ipynb ├── 02-Analysis.ipynb ├── input ├── FoxP_monomer.contacts └── FoxP_monomer.pdb ├── other_notebooks ├── Chapman_Kolmogorov.ipynb ├── getTStrajectory.ipynb └── radiusOfGyration.ipynb └── output ├── 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