├── .gitignore ├── .readthedocs.yml ├── .travis.yml ├── LICENSE ├── README.md ├── conda-recipe ├── conda_build_config.yaml └── meta.yaml ├── docs └── source │ ├── changelog.rst │ ├── conf.py │ ├── environment.yml │ ├── examples.bpti-ncmc.rst │ ├── examples.bpti.rst │ ├── examples.rst │ ├── examples.scytalone.rst │ ├── examples.water.rst │ ├── grand.potential.rst │ ├── grand.rst │ ├── grand.samplers.rst │ ├── grand.utils.rst │ ├── index.rst │ ├── intro.rst │ └── modules.rst ├── examples ├── bpti-ncmc │ ├── bpti-equil.pdb │ └── bpti-ncmc.py ├── bpti │ ├── README.md │ ├── equil │ │ ├── bpti.pdb │ │ ├── equil-npt.py │ │ ├── equil-uvt1.py │ │ └── equil-uvt2.py │ └── prod │ │ ├── bpti-equil.pdb │ │ ├── bpti-restart.py │ │ └── bpti.py ├── scytalone │ ├── mq1.prepi │ ├── mq1.prmtop │ ├── scytalone-equil.pdb │ └── scytalone.py └── water │ ├── water.py │ └── water_box-eq.pdb ├── grand ├── __init__.py ├── data │ ├── tests │ │ ├── benzene.pdb │ │ ├── benzene.prepi │ │ ├── benzene.prmtop │ │ ├── bpti-ghost-wats.txt │ │ ├── bpti-ghosts.pdb │ │ ├── bpti-raw.dcd │ │ ├── bpti.pdb │ │ ├── mq1.frcmod │ │ ├── mq1.prepi │ │ ├── scytalone.pdb │ │ ├── water-ghosts.pdb │ │ └── water_box-eq.pdb │ └── tip3p.pdb ├── potential.py ├── samplers.py ├── scripts │ └── gcmc_pymol.py ├── tests │ ├── __init__.py │ ├── test_potential.py │ ├── test_samplers.py │ └── test_utils.py └── utils.py ├── setup.cfg └── setup.py /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/essex-lab/grand/HEAD/.gitignore -------------------------------------------------------------------------------- /.readthedocs.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/essex-lab/grand/HEAD/.readthedocs.yml -------------------------------------------------------------------------------- /.travis.yml: -------------------------------------------------------------------------------- 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