├── .coveragerc ├── .git-blame-ignore-revs ├── .gitattributes ├── .github └── workflows │ ├── black.yaml │ ├── ci.yaml │ └── deploy.yaml ├── .gitignore ├── .readthedocs.yaml ├── .vscode ├── extensions.json └── settings.json ├── AUTHORS ├── CHANGES ├── COPYING ├── INSTALL.rst ├── MANIFEST.in ├── README.rst ├── devtools └── conda-envs │ ├── readthedocs.yaml │ └── test_env.yaml ├── doc ├── examples │ ├── README.rst │ ├── benzene.yml │ ├── benzene │ │ ├── README.txt │ │ ├── benzene.itp │ │ ├── benzene.pdb │ │ ├── benzene.pdb.png │ │ ├── dVdl.pdf │ │ └── session.py │ └── martini │ │ ├── benzene.pdb │ │ ├── em.mdp │ │ ├── eq.mdp │ │ ├── martini-benzene.ipynb │ │ ├── octanol.gro │ │ ├── run.mdp │ │ └── water.gro ├── logo │ ├── LICENSE │ ├── mdpow-ico-32x32.pdf │ ├── mdpow-ico-32x32.tif │ ├── mdpow-logo.pdf │ ├── mdpow.ico │ └── pow-1601674_640.png ├── requirements.txt └── sphinx │ ├── Makefile │ └── source │ ├── INSTALL.txt │ ├── _static │ ├── mdpow-logo.png │ └── mdpow.ico │ ├── analysis.txt │ ├── analysis │ ├── dihedral.txt │ ├── ensemble.txt │ ├── ensemble_analysis.txt │ └── solvation.txt │ ├── conf.py │ ├── equil.txt │ ├── fep.txt │ ├── forcefields.txt │ ├── index.txt │ ├── init.txt │ ├── scripts.txt │ ├── tutorials │ └── workflows-tutorials_automated-dihedrals.ipynb │ ├── utilities.txt │ ├── workflows.txt │ └── workflows │ ├── base.txt │ ├── dihedrals.txt │ └── registry.txt ├── mdpow ├── __init__.py ├── _version.py ├── analysis │ ├── __init__.py │ ├── dihedral.py │ ├── ensemble.py │ └── solvation.py ├── config.py ├── equil.py ├── fep.py ├── filelock.py ├── forcefields.py ├── log.py ├── restart.py ├── run.py ├── solventdata.yml ├── templates │ ├── NPT_amber.mdp │ ├── NPT_charmm.mdp │ ├── NPT_opls.mdp │ ├── bar_amber.mdp │ ├── bar_charmm.mdp │ ├── bar_opls.mdp │ ├── em_amber.mdp │ ├── em_charmm.mdp │ ├── em_opls.mdp │ ├── runinput.yml │ ├── system.top.template │ └── system_octwet.top.template ├── tests │ ├── __init__.py │ ├── tempdir.py │ ├── test_Gsolv.py │ ├── test_analysis.py │ ├── test_analysis_alchemlyb.py │ ├── test_automated_dihedral_analysis.py │ ├── test_config.py │ ├── test_dihedral.py │ ├── test_ensemble.py │ ├── test_equilibration_script.py │ ├── test_fep.py │ ├── test_fep_analysis.py │ ├── test_fep_script.py │ ├── test_filelock.py │ ├── test_forcefields.py │ ├── test_journals.py │ ├── test_run.py │ ├── test_runinput.py │ ├── test_solv_shell.py │ ├── test_solvation.py │ ├── test_version.py │ ├── test_workflows_base.py │ ├── test_workflows_registry.py │ └── testing_resources │ │ ├── manifest.yml │ │ ├── molecules │ │ └── benzene │ │ │ ├── benzene.itp │ │ │ ├── benzene.pdb │ │ │ ├── benzene_amber.itp │ │ │ └── benzene_charmm.itp │ │ ├── states │ │ ├── FEP │ │ │ └── benzene │ │ │ │ └── FEP │ │ │ │ └── water │ │ │ │ ├── Coulomb │ │ │ │ ├── 1000 │ │ │ │ │ ├── md.edr │ │ │ │ │ └── md.tpr │ │ │ │ ├── 0000 │ │ │ │ │ ├── md.edr │ │ │ │ │ └── md.tpr │ │ │ │ ├── 0250 │ │ │ │ │ ├── md.edr │ │ │ │ │ └── md.tpr │ │ │ │ ├── 0500 │ │ │ │ │ ├── md.edr │ │ │ │ │ └── md.tpr │ │ │ │ └── 0750 │ │ │ │ │ ├── md.edr │ │ │ │ │ └── md.tpr │ │ │ │ ├── Gsolv.fep │ │ │ │ └── VDW │ │ │ │ ├── 1000 │ │ │ │ ├── md.edr │ │ │ │ └── md.tpr │ │ │ │ ├── 0000 │ │ │ │ ├── md.edr │ │ │ │ └── md.tpr │ │ │ │ ├── 0050 │ │ │ │ ├── md.edr │ │ │ │ └── md.tpr │ │ │ │ ├── 0100 │ │ │ │ ├── md.edr │ │ │ │ └── md.tpr │ │ │ │ ├── 0200 │ │ │ │ ├── md.edr │ │ │ │ └── md.tpr │ │ │ │ ├── 0300 │ │ │ │ ├── md.edr │ │ │ │ └── md.tpr │ │ │ │ ├── 0400 │ │ │ │ ├── md.edr │ │ │ │ └── md.tpr │ │ │ │ ├── 0500 │ │ │ │ ├── md.edr │ │ │ │ └── md.tpr │ │ │ │ ├── 0600 │ │ │ │ ├── md.edr │ │ │ │ └── md.tpr │ │ │ │ ├── 0650 │ │ │ │ ├── md.edr │ │ │ │ └── md.tpr │ │ │ │ ├── 0700 │ │ │ │ ├── md.edr │ │ │ │ └── md.tpr │ │ │ │ ├── 0750 │ │ │ │ ├── md.edr │ │ │ │ └── md.tpr │ │ │ │ ├── 0800 │ │ │ │ ├── md.edr │ │ │ │ └── md.tpr │ │ │ │ ├── 0850 │ │ │ │ ├── md.edr │ │ │ │ └── md.tpr │ │ │ │ ├── 0900 │ │ │ │ ├── md.edr │ │ │ │ └── md.tpr │ │ │ │ └── 0950 │ │ │ │ ├── md.edr │ │ │ │ └── md.tpr │ │ ├── base │ │ │ ├── benzene.itp │ │ │ ├── benzene.pdb │ │ │ └── runinput.yml │ │ ├── example_FEP │ │ │ └── FEP │ │ │ │ ├── md.gro │ │ │ │ ├── test_solv │ │ │ │ └── Coulomb │ │ │ │ │ ├── 1000 │ │ │ │ │ ├── md.gro │ │ │ │ │ └── md_red.xtc │ │ │ │ │ └── 0000 │ │ │ │ │ └── test.txt │ │ │ │ └── water │ │ │ │ ├── Coulomb │ │ │ │ ├── 1000 │ │ │ │ │ ├── md.gro.bz2 │ │ │ │ │ └── md_red.xtc │ │ │ │ ├── 0000 │ │ │ │ │ ├── md.gro │ │ │ │ │ ├── md.tpr │ │ │ │ │ └── md_red.xtc │ │ │ │ └── 0500 │ │ │ │ │ ├── md.gro.bz2 │ │ │ │ │ └── md_red.xtc │ │ │ │ └── VDW │ │ │ │ ├── 1000 │ │ │ │ ├── md.gro.gz │ │ │ │ └── md_red.xtc │ │ │ │ ├── 0000 │ │ │ │ ├── md.gro.bz2 │ │ │ │ └── md_red.xtc │ │ │ │ ├── 0250 │ │ │ │ ├── md.gro.bz2 │ │ │ │ └── md_red.xtc │ │ │ │ └── 0500 │ │ │ │ ├── md.gro.bz2 │ │ │ │ └── md_red.xtc │ │ ├── md_npt │ │ │ ├── benzene.itp │ │ │ ├── benzene.pdb │ │ │ ├── benzene │ │ │ │ ├── Equilibrium │ │ │ │ │ └── water │ │ │ │ │ │ ├── MD_NPT │ │ │ │ │ │ ├── local.sh │ │ │ │ │ │ ├── md.gro │ │ │ │ │ │ ├── md.mdp │ │ │ │ │ │ ├── processed.top │ │ │ │ │ │ └── residuetypes.dat │ │ │ │ │ │ ├── MD_relaxed │ │ │ │ │ │ ├── local.sh │ │ │ │ │ │ ├── md.gro │ │ │ │ │ │ ├── md.mdp │ │ │ │ │ │ ├── mdout.mdp │ │ │ │ │ │ ├── processed.top │ │ │ │ │ │ └── residuetypes.dat │ │ │ │ │ │ ├── em │ │ │ │ │ │ ├── em.mdp │ │ │ │ │ │ ├── em.pdb │ │ │ │ │ │ ├── mdout.mdp │ │ │ │ │ │ └── processed.top │ │ │ │ │ │ ├── solvation │ │ │ │ │ │ ├── boxed.gro │ │ │ │ │ │ ├── compact.pdb │ │ │ │ │ │ ├── ionized.gro │ │ │ │ │ │ ├── main.ndx │ │ │ │ │ │ ├── mdout.mdp │ │ │ │ │ │ ├── none.mdp │ │ │ │ │ │ └── solvated.gro │ │ │ │ │ │ └── top │ │ │ │ │ │ ├── benzene.itp │ │ │ │ │ │ ├── pp_system.top │ │ │ │ │ │ └── system.top │ │ │ │ └── water.simulation │ │ │ └── runinput.yml │ │ └── workflows │ │ │ ├── SM25 │ │ │ └── FEP │ │ │ │ └── water │ │ │ │ ├── Coulomb │ │ │ │ ├── 1000 │ │ │ │ │ ├── md.tpr │ │ │ │ │ └── md.xtc │ │ │ │ ├── 0000 │ │ │ │ │ ├── md.tpr │ │ │ │ │ └── md.xtc │ │ │ │ └── 0500 │ │ │ │ │ ├── md.tpr │ │ │ │ │ └── md.xtc │ │ │ │ └── VDW │ │ │ │ ├── 1000 │ │ │ │ ├── md.tpr │ │ │ │ └── md.xtc │ │ │ │ ├── 0000 │ │ │ │ ├── md.tpr │ │ │ │ └── md.xtc │ │ │ │ ├── 0200 │ │ │ │ ├── md.tpr │ │ │ │ └── md.xtc │ │ │ │ └── 0500 │ │ │ │ ├── md.tpr │ │ │ │ └── md.xtc │ │ │ ├── SM26 │ │ │ └── FEP │ │ │ │ └── water │ │ │ │ ├── Coulomb │ │ │ │ ├── 1000 │ │ │ │ │ ├── md.tpr │ │ │ │ │ └── md.xtc │ │ │ │ ├── 0000 │ │ │ │ │ ├── md.tpr │ │ │ │ │ └── md.xtc │ │ │ │ └── 0500 │ │ │ │ │ ├── md.tpr │ │ │ │ │ └── md.xtc │ │ │ │ └── VDW │ │ │ │ ├── 1000 │ │ │ │ ├── md.tpr │ │ │ │ └── md.xtc │ │ │ │ ├── 0000 │ │ │ │ ├── md.tpr │ │ │ │ └── md.xtc │ │ │ │ ├── 0200 │ │ │ │ ├── md.tpr │ │ │ │ └── md.xtc │ │ │ │ └── 0500 │ │ │ │ ├── md.tpr │ │ │ │ └── md.xtc │ │ │ └── project_paths.csv │ │ └── test_configurations │ │ └── altered_runinput.yml ├── top │ ├── 1cyclo.gro │ ├── 1cyclo_amber.gro │ ├── 1cyclo_charmm.gro │ ├── 1oct.gro │ ├── 1oct_amber.gro │ ├── 1oct_charmm.gro │ ├── 1octwet.gro │ ├── 1octwet_amber.gro │ ├── 1octwet_charmm.gro │ ├── 1tol_amber.gro │ ├── 1tol_charmm.gro │ ├── 1tol_oplsaa.gro │ ├── amber99sb.ff │ │ ├── 1cyclo.itp │ │ ├── 1oct.itp │ │ ├── 1octwet.itp │ │ ├── 1tol.itp │ │ ├── aminoacids.arn │ │ ├── aminoacids.c.tdb │ │ ├── aminoacids.hdb │ │ ├── aminoacids.n.tdb │ │ ├── aminoacids.r2b │ │ ├── aminoacids.rtp │ │ ├── aminoacids.vsd │ │ ├── atomtypes.atp │ │ ├── dna.arn │ │ ├── dna.hdb │ │ ├── dna.r2b │ │ ├── dna.rtp │ │ ├── ffbonded.itp │ │ ├── ffnonbonded.itp │ │ ├── forcefield.doc │ │ ├── forcefield.itp │ │ ├── gaff2_nonbonded.itp │ │ ├── gbsa.itp │ │ ├── ions.itp │ │ ├── rna.arn │ │ ├── rna.hdb │ │ ├── rna.r2b │ │ ├── rna.rtp │ │ ├── spc.itp │ │ ├── spce.itp │ │ ├── tip3p.itp │ │ ├── tip4p.itp │ │ ├── tip4pew.itp │ │ ├── tip5p.itp │ │ ├── urea.itp │ │ └── watermodels.dat │ ├── atommass.dat │ ├── charmm36-mar2019.ff │ │ ├── 1cyclo.itp │ │ ├── 1oct.itp │ │ ├── 1octwet.itp │ │ ├── 1tol.itp │ │ ├── atomtypes.atp │ │ ├── cmap.itp │ │ ├── ffbonded.itp │ │ ├── ffnonbonded.itp │ │ ├── forcefield.doc │ │ ├── forcefield.itp │ │ ├── gb.itp │ │ ├── ions.itp │ │ ├── merged.arn │ │ ├── merged.c.tdb │ │ ├── merged.hdb │ │ ├── merged.n.tdb │ │ ├── merged.r2b │ │ ├── merged.rtp │ │ ├── merged.vsd │ │ ├── nbfix.itp │ │ ├── old_c36_cmap.itp │ │ ├── spc.itp │ │ ├── spce.itp │ │ ├── tip3p.itp │ │ ├── tip4p.itp │ │ ├── tip5p.itp │ │ └── watermodels.dat │ ├── elements.dat │ ├── ffoplsaa.itp │ ├── oplsaa.ff │ │ ├── 1cyclo.itp │ │ ├── 1oct.itp │ │ ├── 1octnew.itp │ │ ├── 1octwet.itp │ │ ├── 1octwetnew.itp │ │ ├── 1propanol.itp │ │ ├── 1tol.itp │ │ ├── aminoacids.c.tdb │ │ ├── aminoacids.hdb │ │ ├── aminoacids.n.tdb │ │ ├── aminoacids.r2b │ │ ├── aminoacids.rtp │ │ ├── aminoacids.vsd │ │ ├── atomname2type.n2t │ │ ├── atomtypes.atp │ │ ├── ethanol.itp │ │ ├── ffbonded.itp │ │ ├── ffnonbonded.itp │ │ ├── forcefield.doc │ │ ├── forcefield.itp │ │ ├── gbsa.itp │ │ ├── ions.itp │ │ ├── ions_opls.itp │ │ ├── m24.itp │ │ ├── methanol.itp │ │ ├── spc.itp │ │ ├── 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