├── .github └── workflows │ ├── ci-main.yml │ ├── ci-nightly.yml │ ├── gh-pages.yml │ └── test_website.yml ├── .gitignore ├── Makefile ├── README.md ├── conf.py ├── cookbook.rst ├── environment.yml ├── index.rst ├── make.bat ├── notebooks ├── cookbook │ ├── Adding Hydrogens to Nonstandard Molecules.ipynb │ ├── Analyzing Energy Contributions.ipynb │ ├── Applying a Constant External Force.ipynb │ ├── Changing Temperature and Pressure.ipynb │ ├── Computing Interaction Energies.ipynb │ ├── Constraining Atom Positions.ipynb │ ├── Merging Molecules.ipynb │ ├── Querying and Modifying Charges and Other Parameters.ipynb │ ├── Restraining Atom Positions.ipynb │ ├── Restraining Dihedrals.ipynb │ ├── Saving Systems to XML Files.ipynb │ ├── ala_ala_ala.pdb │ ├── first_simulation.ipynb │ ├── report_minimization.ipynb │ └── villin.pdb └── tutorials │ ├── 1AKI-processed.cif │ ├── Alchemical_free_energy_calculations.ipynb │ ├── Running_a_REST_simulation.ipynb │ ├── alanine-dipeptide-water.pdb │ ├── alanine-dipeptide.pdb │ ├── building_systems.ipynb │ ├── cg_ff.xml │ ├── coarse_grained_polymer.ipynb │ ├── constant_potential.ipynb │ ├── constant_potential.pdb │ ├── constant_potential_1.png │ ├── constant_potential_2.png │ ├── constant_potential_3.png │ ├── constant_potential_4.png │ ├── constant_potential_example_gold.xml │ ├── deca-ala.pdb │ ├── deca-alanine.png │ ├── equilibrated_config.png │ ├── getting_started.ipynb │ ├── getting_started_1.png │ ├── getting_started_2.png │ ├── getting_started_3.png │ ├── getting_started_4.png │ ├── hist.png │ ├── initial_config.png │ ├── input.inpcrd │ ├── input.prmtop │ ├── loading_and_reporting.ipynb │ ├── machine_learning_potentials.ipynb │ ├── nuclear_quantum_effects.ipynb │ ├── pmf.png │ ├── simulation_parameters.ipynb │ ├── sine.svg │ ├── umbrella_sampling.ipynb │ ├── umbrella_sampling.svg │ └── villin.pdb ├── sphinx ├── _static │ ├── custom.css │ ├── logo.svg │ └── notebooks.css ├── _templates │ ├── genindex.html │ └── navigation.html 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