├── .gitignore ├── Datasets └── README.md ├── Makefile ├── Models └── README.md ├── README.md ├── Tutorials ├── 1-Tutorial-CG-NNP-Training.ipynb ├── 2-Tutorial-CG-Simulation.ipynb ├── 3-Tutorial-CG-Simulation-analysis.ipynb ├── prior_force_field.yaml ├── simulate.yaml ├── starting_xtc │ ├── a3d_kcenters_32clusters_coords.xtc │ ├── bba_kcenters_32clusters_coords.xtc │ ├── bbl_kcenters_32clusters_coords.xtc │ ├── cln_kcenters_32clusters_coords.xtc │ ├── homeodomain_kcenters_32clusters_coords.xtc │ ├── lambda_kcenters_32clusters_coords.xtc │ ├── ntl9_kcenters_32clusters_coords.xtc │ ├── proteinb_kcenters_32clusters_coords.xtc │ ├── proteing_kcenters_32clusters_coords.xtc │ ├── trp_kcenters_32clusters_coords.xtc │ ├── villin_kcenters_32clusters_coords.xtc │ └── ww_kcenters_32clusters_coords.xtc ├── topology │ ├── a3d.psf │ ├── bba.psf │ ├── bbl.psf │ ├── cln.psf │ ├── homeodomain.psf │ ├── lambda.psf │ ├── ntl9.psf │ ├── proteinb.psf │ ├── proteing.psf │ ├── trp.psf │ ├── villin.psf │ └── 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