├── .codacy.yml ├── .github ├── ISSUE_TEMPLATE │ ├── bug_report.md │ └── feature_request.md ├── pull_request_template.md └── workflows │ ├── lint.yml │ ├── release.yml │ └── test.yml ├── .gitignore ├── ADMIN.rst ├── CHANGES.rst ├── CODE_OF_CONDUCT.md ├── CONTRIBUTING.rst ├── README.md ├── docs ├── Makefile ├── logo_mdgo.svg ├── make.bat ├── mdgo-white.svg └── source │ ├── _static │ ├── logo_mdgo.png │ └── mdgo-white.png │ ├── aqueous.rst │ ├── change_log.rst │ ├── conf.py │ ├── index.rst │ ├── introduction.rst │ ├── latest_changes.rst │ ├── mdgo.conductivity.rst │ ├── mdgo.coordination.rst │ ├── mdgo.core.rst │ ├── mdgo.forcefield.rst │ ├── mdgo.mdgopackmol.rst │ ├── mdgo.msd.rst │ ├── mdgo.residence_time.rst │ ├── mdgo.rst │ ├── mdgo.util.rst │ ├── mdgo.volume.rst │ ├── modules.rst │ └── rtd_requirements.txt ├── mdgo ├── __init__.py ├── conductivity.py ├── coordination.py ├── core │ ├── __init__.py │ ├── analysis.py │ └── run.py ├── forcefield │ ├── __init__.py │ ├── aqueous.py │ ├── charge.py │ ├── crawler.py │ ├── data │ │ ├── ion_lj_params.json │ │ └── water │ │ │ ├── water_opc.lmp │ │ │ ├── water_opc3.lmp │ │ │ ├── water_spc.lmp │ │ │ ├── water_spce.lmp │ │ │ ├── water_tip3p_ew.lmp │ │ │ ├── water_tip3p_fb.lmp │ │ │ ├── water_tip4p_2005.lmp │ │ │ ├── water_tip4p_ew.lmp │ │ │ └── water_tip4p_fb.lmp │ ├── maestro.py │ └── pubchem.py ├── msd.py ├── residence_time.py ├── templates │ ├── mae_cmd_assignbond.txt │ └── mae_cmd_noassignbond.txt └── util │ ├── __init__.py │ ├── coord.py │ ├── dict_utils.py │ ├── num.py │ ├── packmol.py │ ├── reformat.py │ └── volume.py ├── pylintrc ├── pyproject.toml ├── requirements-dev.txt ├── requirements.txt ├── setup.cfg ├── setup.py ├── tasks.py └── tests ├── __init__.py ├── packmol ├── .gitignore ├── AUTHORS ├── LICENSE ├── README.md └── packmol ├── test_conductivity.py ├── test_coordination.py ├── test_core.py ├── test_files ├── C.lmp ├── CCOC(=O)OC.lmp ├── DEC.xyz ├── EC.xyz ├── EMC.gro ├── EMC.itp ├── EMC.lmp ├── EMC.lmp.xyz 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