├── .codecov.yml ├── .github ├── CONTRIBUTING.md └── PULL_REQUEST_TEMPLATE.md ├── .gitignore ├── .lgtm.yml ├── .travis.yml ├── CODE_OF_CONDUCT.md ├── LICENSE ├── MANIFEST.in ├── README.md ├── REMD_analysis ├── HREMD_get_dhdl.sh ├── HREMD_prep.sh ├── REMD.py ├── REMD_analysis.py ├── REMD_conf_prep.py ├── REMD_tpr_prep.py ├── Result.txt ├── __init__.py ├── _version.py ├── calculate_free_energy.py ├── data │ ├── README.md │ └── look_and_say.dat ├── deprecated_REMD_free_energy.py ├── examples │ ├── hist_diag_PLCpep7.png │ ├── state_time_PLCpep7.png │ └── transition_matrix_PLCpep7.png └── tests │ ├── __init__.py │ └── test_REMD_analysis.py ├── appveyor.yml ├── devtools ├── README.md ├── conda-envs │ └── test_env.yaml ├── scripts │ └── create_conda_env.py └── travis-ci │ └── before_install.sh ├── docs ├── Makefile ├── README.md ├── _static │ └── README.md ├── _templates │ └── README.md ├── api.rst ├── conf.py ├── getting_started.rst ├── index.rst └── make.bat ├── setup.cfg ├── setup.py └── 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