├── .gitattributes ├── .gitignore ├── PEG-in-vacuum ├── PEG.jpg ├── README.md ├── ff │ ├── charmm35r.itp │ └── peg.itp ├── inputs │ └── nvt.mdp ├── peg.gro └── topol.top ├── README.md ├── sodium_chloride_solution ├── NaCl.jpg ├── README.md ├── build │ ├── .ipynb_checkpoints │ │ └── generate_configuration_gromacs-checkpoint.ipynb │ ├── build_multiple_folder.sh │ └── generate_configuration_gromacs.ipynb ├── cs_5M │ ├── conf.gro │ └── topol.top ├── ff │ ├── atomtypes.atp │ ├── ffbonded.itp │ ├── ffnonbonded.itp │ ├── forcefield.itp │ ├── ions.itp │ ├── molecules.rtp │ └── tip4peps.itp └── input │ ├── npt.mdp │ ├── nvt.mdp │ └── prod.mdp ├── water-in-box ├── README.md ├── bulkwater.jpg ├── conf.gro ├── diff_coeff_mda.py ├── ff │ ├── forcefield.itp │ └── tip4peps.itp ├── generate_system.py ├── input │ ├── npt.mdp │ ├── nvt.mdp │ ├── run.mdp │ └── visco.mdp └── topol.top └── water-in-salt-slit ├── Na2SO4_1M ├── ConfigurationGenerator.py ├── Na2SO4 │ ├── Angle.dat │ ├── Bond.dat │ └── Position.dat ├── conf.gro ├── log.err ├── log.out ├── npt.mdp ├── npt.top ├── run_bigfoot_pore.sh ├── runall.sh └── topol.top ├── NaCl_0M ├── ConfigurationGenerator.py ├── NaCl │ └── Position.dat ├── conf.gro ├── log.err ├── log.out ├── npt.mdp ├── npt.top ├── run_bigfoot_pore.sh ├── runall.sh └── topol.top ├── NaCl_1M ├── ConfigurationGenerator.py ├── NaCl │ └── Position.dat ├── conf.gro ├── log.err ├── log.out ├── npt.mdp ├── npt.top ├── run_bigfoot_pore.sh ├── runall.sh └── topol.top ├── NaCl_4M ├── ConfigurationGenerator.py ├── NaCl │ └── Position.dat ├── conf.gro ├── energy.xvg ├── log.err ├── log.out ├── npt.mdp ├── npt.top ├── nvt.cpt ├── nvt.edr ├── nvt.log ├── nvt.mdp ├── nvt.top ├── nvt.tpr ├── run_bigfoot_pore.sh ├── runall.sh ├── state.vmd └── topol.top ├── README.md ├── ff ├── atomtypes.atp ├── ffbonded.itp ├── ffnonbonded.itp ├── forcefield.itp ├── ions.itp ├── molecules.rtp └── tip4peps.itp └── input ├── npt.mdp ├── nvt.mdp ├── prodHR.mdp └── prodLR.mdp /.gitattributes: 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