├── .gitignore ├── Licence.md ├── MD_simulation_on_alanine_dipeptide └── current_work │ ├── .gitignore │ ├── README.md │ ├── resources │ └── .gitignore │ ├── snapshot.sh │ ├── src │ ├── .gitignore │ ├── ANN_simulation.py │ ├── autoencoders.py │ ├── biased_simulation.py │ ├── biased_simulation_general.py │ ├── config.py │ ├── coordinates_data_files_list.py │ ├── generate_coordinates.py │ ├── helper_func.py │ ├── kernel_tica.py │ ├── main_work.py │ ├── molecule_spec_sutils.py │ ├── remove_water_mol.py │ ├── structural_alignment.py │ ├── tf_load.py │ ├── train_network_and_save_for_iter.py │ └── workqueue.py │ ├── target │ └── .gitignore │ └── tests │ ├── .gitignore │ ├── ANN_simulation_test.py │ └── Makefile ├── README.md ├── archive └── plumed_adp.zip └── figures ├── autoencoder_1.png ├── autoencoder_2.png ├── diagram_autoencoder.png └── hierarchical_autoencoder.png /.gitignore: -------------------------------------------------------------------------------- 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