├── LICENSE ├── README.md ├── examples ├── .ipynb_checkpoints │ └── example_analysis-checkpoint.ipynb ├── README.md ├── analysis_openbpmd.py ├── example_analysis.ipynb ├── example_analysis.py ├── output │ ├── rep_0 │ │ └── bpm_results.csv │ ├── rep_1 │ │ └── bpm_results.csv │ ├── rep_2 │ │ └── bpm_results.csv │ ├── rep_3 │ │ └── bpm_results.csv │ ├── rep_4 │ │ └── bpm_results.csv │ ├── rep_5 │ │ └── bpm_results.csv │ ├── rep_6 │ │ └── bpm_results.csv │ ├── rep_7 │ │ └── bpm_results.csv │ ├── rep_8 │ │ └── bpm_results.csv │ ├── rep_9 │ │ └── bpm_results.csv │ └── results.csv ├── solvated.gro ├── solvated.pdb ├── solvated.prm7 ├── solvated.rst7 └── solvated.top ├── openbpmd.py └── tests ├── files ├── .ipynb_checkpoints │ └── Untitled-checkpoint.ipynb ├── equil_system.pdb ├── minimized_system.pdb ├── reference_score_arrs.npy ├── rep_0 │ └── bpm_results.csv ├── rep_1 │ └── bpm_results.csv ├── rep_2 │ └── bpm_results.csv ├── rep_3 │ └── bpm_results.csv ├── rep_4 │ └── bpm_results.csv ├── rep_5 │ └── bpm_results.csv ├── rep_6 │ └── bpm_results.csv ├── rep_7 │ └── bpm_results.csv ├── rep_8 │ └── bpm_results.csv ├── rep_9 │ └── bpm_results.csv ├── solute.dcd ├── solute.pdb ├── solvated.prm7 └── solvated.rst7 └── test_openbpmd.py /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Gervasiolab/OpenBPMD/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Gervasiolab/OpenBPMD/HEAD/README.md -------------------------------------------------------------------------------- /examples/.ipynb_checkpoints/example_analysis-checkpoint.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Gervasiolab/OpenBPMD/HEAD/examples/.ipynb_checkpoints/example_analysis-checkpoint.ipynb -------------------------------------------------------------------------------- /examples/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Gervasiolab/OpenBPMD/HEAD/examples/README.md -------------------------------------------------------------------------------- /examples/analysis_openbpmd.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Gervasiolab/OpenBPMD/HEAD/examples/analysis_openbpmd.py -------------------------------------------------------------------------------- /examples/example_analysis.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Gervasiolab/OpenBPMD/HEAD/examples/example_analysis.ipynb -------------------------------------------------------------------------------- /examples/example_analysis.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Gervasiolab/OpenBPMD/HEAD/examples/example_analysis.py -------------------------------------------------------------------------------- /examples/output/rep_0/bpm_results.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Gervasiolab/OpenBPMD/HEAD/examples/output/rep_0/bpm_results.csv -------------------------------------------------------------------------------- /examples/output/rep_1/bpm_results.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Gervasiolab/OpenBPMD/HEAD/examples/output/rep_1/bpm_results.csv -------------------------------------------------------------------------------- /examples/output/rep_2/bpm_results.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Gervasiolab/OpenBPMD/HEAD/examples/output/rep_2/bpm_results.csv -------------------------------------------------------------------------------- /examples/output/rep_3/bpm_results.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Gervasiolab/OpenBPMD/HEAD/examples/output/rep_3/bpm_results.csv -------------------------------------------------------------------------------- /examples/output/rep_4/bpm_results.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Gervasiolab/OpenBPMD/HEAD/examples/output/rep_4/bpm_results.csv -------------------------------------------------------------------------------- /examples/output/rep_5/bpm_results.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Gervasiolab/OpenBPMD/HEAD/examples/output/rep_5/bpm_results.csv -------------------------------------------------------------------------------- /examples/output/rep_6/bpm_results.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Gervasiolab/OpenBPMD/HEAD/examples/output/rep_6/bpm_results.csv -------------------------------------------------------------------------------- /examples/output/rep_7/bpm_results.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Gervasiolab/OpenBPMD/HEAD/examples/output/rep_7/bpm_results.csv -------------------------------------------------------------------------------- /examples/output/rep_8/bpm_results.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Gervasiolab/OpenBPMD/HEAD/examples/output/rep_8/bpm_results.csv -------------------------------------------------------------------------------- /examples/output/rep_9/bpm_results.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Gervasiolab/OpenBPMD/HEAD/examples/output/rep_9/bpm_results.csv -------------------------------------------------------------------------------- /examples/output/results.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Gervasiolab/OpenBPMD/HEAD/examples/output/results.csv -------------------------------------------------------------------------------- /examples/solvated.gro: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Gervasiolab/OpenBPMD/HEAD/examples/solvated.gro -------------------------------------------------------------------------------- /examples/solvated.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Gervasiolab/OpenBPMD/HEAD/examples/solvated.pdb -------------------------------------------------------------------------------- /examples/solvated.prm7: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Gervasiolab/OpenBPMD/HEAD/examples/solvated.prm7 -------------------------------------------------------------------------------- /examples/solvated.rst7: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Gervasiolab/OpenBPMD/HEAD/examples/solvated.rst7 -------------------------------------------------------------------------------- /examples/solvated.top: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Gervasiolab/OpenBPMD/HEAD/examples/solvated.top -------------------------------------------------------------------------------- /openbpmd.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Gervasiolab/OpenBPMD/HEAD/openbpmd.py -------------------------------------------------------------------------------- /tests/files/.ipynb_checkpoints/Untitled-checkpoint.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Gervasiolab/OpenBPMD/HEAD/tests/files/.ipynb_checkpoints/Untitled-checkpoint.ipynb -------------------------------------------------------------------------------- /tests/files/equil_system.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Gervasiolab/OpenBPMD/HEAD/tests/files/equil_system.pdb -------------------------------------------------------------------------------- /tests/files/minimized_system.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Gervasiolab/OpenBPMD/HEAD/tests/files/minimized_system.pdb -------------------------------------------------------------------------------- /tests/files/reference_score_arrs.npy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Gervasiolab/OpenBPMD/HEAD/tests/files/reference_score_arrs.npy -------------------------------------------------------------------------------- /tests/files/rep_0/bpm_results.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Gervasiolab/OpenBPMD/HEAD/tests/files/rep_0/bpm_results.csv -------------------------------------------------------------------------------- /tests/files/rep_1/bpm_results.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Gervasiolab/OpenBPMD/HEAD/tests/files/rep_1/bpm_results.csv -------------------------------------------------------------------------------- /tests/files/rep_2/bpm_results.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Gervasiolab/OpenBPMD/HEAD/tests/files/rep_2/bpm_results.csv -------------------------------------------------------------------------------- /tests/files/rep_3/bpm_results.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Gervasiolab/OpenBPMD/HEAD/tests/files/rep_3/bpm_results.csv -------------------------------------------------------------------------------- /tests/files/rep_4/bpm_results.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Gervasiolab/OpenBPMD/HEAD/tests/files/rep_4/bpm_results.csv -------------------------------------------------------------------------------- /tests/files/rep_5/bpm_results.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Gervasiolab/OpenBPMD/HEAD/tests/files/rep_5/bpm_results.csv -------------------------------------------------------------------------------- /tests/files/rep_6/bpm_results.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Gervasiolab/OpenBPMD/HEAD/tests/files/rep_6/bpm_results.csv -------------------------------------------------------------------------------- /tests/files/rep_7/bpm_results.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Gervasiolab/OpenBPMD/HEAD/tests/files/rep_7/bpm_results.csv -------------------------------------------------------------------------------- /tests/files/rep_8/bpm_results.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Gervasiolab/OpenBPMD/HEAD/tests/files/rep_8/bpm_results.csv -------------------------------------------------------------------------------- /tests/files/rep_9/bpm_results.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Gervasiolab/OpenBPMD/HEAD/tests/files/rep_9/bpm_results.csv -------------------------------------------------------------------------------- /tests/files/solute.dcd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Gervasiolab/OpenBPMD/HEAD/tests/files/solute.dcd -------------------------------------------------------------------------------- /tests/files/solute.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Gervasiolab/OpenBPMD/HEAD/tests/files/solute.pdb -------------------------------------------------------------------------------- /tests/files/solvated.prm7: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Gervasiolab/OpenBPMD/HEAD/tests/files/solvated.prm7 -------------------------------------------------------------------------------- /tests/files/solvated.rst7: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Gervasiolab/OpenBPMD/HEAD/tests/files/solvated.rst7 -------------------------------------------------------------------------------- /tests/test_openbpmd.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Gervasiolab/OpenBPMD/HEAD/tests/test_openbpmd.py --------------------------------------------------------------------------------