├── .codecov.yml ├── .git-blame-ignore-revs ├── .gitattributes ├── .github ├── CONTRIBUTING.md ├── PULL_REQUEST_TEMPLATE.md └── workflows │ ├── CI.yml │ └── gpu-runner.yaml ├── .gitignore ├── .lgtm.yml ├── CODE_OF_CONDUCT.md ├── LICENSE ├── MANIFEST.in ├── README.md ├── devtools ├── README.md └── conda-envs │ └── test_env.yaml ├── docs ├── Makefile ├── _static │ └── images │ │ ├── logo.jpg │ │ └── logo.png ├── alchemy.rst ├── cache.rst ├── conf.py ├── devtutorial.rst ├── environment.yml ├── forcefactories.rst ├── forces.rst ├── gettingstarted.rst ├── index.rst ├── installation.rst ├── integrators.rst ├── make.bat ├── mcmc.rst ├── multistate.rst ├── references.bib ├── references.rst ├── releasehistory.rst ├── scripts.rst ├── states.rst ├── storage.rst ├── testsystems.rst └── utils.rst ├── examples ├── README.md └── integrator-benchmarks │ └── integrator-benchmarks.py ├── openmmtools ├── __init__.py ├── _version.py ├── alchemy │ ├── __init__.py │ └── alchemy.py ├── cache.py ├── constants.py ├── data │ ├── T4-lysozyme-L99A-implicit │ │ ├── complex-min.sander.out │ │ ├── complex-minimized.crd │ │ ├── complex-testenergy.sander.out │ │ ├── complex.crd │ │ ├── complex.pdb │ │ ├── complex.prmtop │ │ ├── leap.log │ │ ├── ligand-min.sander.out │ │ ├── ligand-minimized.crd │ │ ├── ligand-testenergy.sander.out │ │ ├── ligand.crd │ │ ├── ligand.frcmod │ │ ├── ligand.mol2 │ │ ├── ligand.pdb │ │ ├── ligand.prmtop │ │ ├── ligand.tripos.mol2 │ │ ├── mdinfo │ │ ├── min.sander.in │ │ ├── receptor-min.sander.out │ │ ├── receptor-minimized.crd │ │ ├── receptor-testenergy.sander.out │ │ ├── receptor.crd │ │ ├── receptor.pdb │ │ ├── receptor.prmtop │ │ ├── setup.leap.in │ │ ├── setup.leap.out │ │ └── testenergy.sander.in │ ├── alanine-dipeptide-explicit │ │ ├── alanine-dipeptide.crd │ │ ├── alanine-dipeptide.pdb │ │ ├── alanine-dipeptide.prmtop │ │ ├── generate-pdb.py │ │ ├── leap.log │ │ ├── run.sh │ │ └── setup.leap.in │ ├── alanine-dipeptide-gbsa │ │ ├── README │ │ ├── alanine-dipeptide.crd │ │ ├── alanine-dipeptide.pdb │ │ ├── alanine-dipeptide.prmtop │ │ ├── leap.log │ │ ├── run.sh │ │ └── setup.leap.in │ ├── amoeba │ │ ├── 1AP4_14_wat.pdb │ │ └── ion-in-water.pdb │ ├── benzene-toluene-implicit │ │ ├── benzene.frcmod │ │ ├── benzene.gaff.mol2 │ │ ├── complex.inpcrd │ │ ├── complex.pdb │ │ ├── complex.prmtop │ │ ├── generate-molecules.py │ │ ├── receptor.inpcrd │ │ ├── receptor.pdb │ │ ├── receptor.prmtop │ │ ├── setup.leap.in │ │ ├── setup.sh │ │ ├── solvent.inpcrd │ │ ├── solvent.pdb │ │ └── solvent.prmtop │ ├── cb7-b2 │ │ ├── README.md │ │ ├── b2_am1-bcc.frcmod │ │ ├── b2_am1-bcc.mol2 │ │ ├── b2_tripos.mol2 │ │ ├── cb7_am1-bcc.frcmod │ │ ├── cb7_am1-bcc.mol2 │ │ ├── cb7_b2.pdb │ │ ├── cb7_tripos.mol2 │ │ ├── complex-explicit.inpcrd │ │ ├── complex-explicit.pdb │ │ ├── complex-explicit.prmtop │ │ ├── complex-vacuum.inpcrd │ │ ├── complex-vacuum.pdb │ │ ├── complex-vacuum.prmtop │ │ ├── leap.log │ │ ├── ligand.inpcrd │ │ ├── ligand.pdb │ │ ├── ligand.prmtop │ │ ├── receptor.inpcrd │ │ ├── receptor.pdb │ │ ├── receptor.prmtop │ │ ├── setup.leap.in │ │ ├── setup.sh │ │ └── water.pdb │ ├── cb7-viologen │ │ ├── README.md │ │ ├── leap │ │ │ ├── CB7.frcmod │ │ │ ├── CB7.gaff.mol2 │ │ │ ├── CB7.tripos.mol2 │ │ │ ├── complex-explicit.inpcrd │ │ │ ├── complex-explicit.pdb │ │ │ ├── complex-explicit.prmtop │ │ │ ├── complex-vacuum.inpcrd │ │ │ ├── complex-vacuum.pdb │ │ │ ├── complex-vacuum.prmtop │ │ │ ├── complex.inpcrd │ │ │ ├── leap.log │ │ │ ├── ligand.inpcrd │ │ │ ├── ligand.pdb │ │ │ ├── ligand.prmtop │ │ │ ├── receptor.inpcrd │ │ │ ├── receptor.pdb │ │ │ ├── receptor.prmtop │ │ │ ├── setup.leap.in │ │ │ ├── setup.sh │ │ │ ├── solvent.inpcrd │ │ │ ├── vacuum.inpcrd │ │ │ ├── viologen.frcmod │ │ │ ├── viologen.gaff.mol2 │ │ │ └── viologen.tripos.mol2 │ │ ├── molecules │ │ │ ├── CB7.tripos.mol2 │ │ │ ├── README.md │ │ │ ├── create-viologen.py │ │ │ └── viologen.tripos.mol2 │ │ └── references │ │ │ └── kaifer-viologen-association.pdf │ ├── dhfr │ │ ├── JAC.inpcrd │ │ ├── JAC.prmtop │ │ ├── README.md │ │ └── system.pdb │ ├── dna_dodecamer_explicit │ │ ├── 4c64_no_mg.pdb │ │ ├── README.md │ │ ├── inpcrd │ │ ├── leap.in │ │ ├── minimize.py │ │ ├── minimized_dna_dodecamer.pdb │ │ └── prmtop │ ├── methanol-box │ │ ├── README │ │ ├── methanol-box.crd │ │ ├── methanol-box.pdb │ │ └── methanol-box.prmtop │ ├── reporter-examples │ │ ├── alanine_dipeptide_legacy.nc │ │ └── alanine_dipeptide_legacy_checkpoint.nc │ ├── src-explicit │ │ ├── 1yi6-minimized.pdb │ │ ├── 1yi6-pdbfixer.pdb │ │ ├── README.md │ │ ├── integrator.xml │ │ ├── prepare_pdb.py │ │ ├── state.xml │ │ └── system.xml │ ├── src-implicit │ │ ├── 1yi6-minimized.pdb │ │ ├── 1yi6-pdbfixer.pdb │ │ ├── README.md │ │ ├── integrator.xml │ │ ├── prepare_pdb.py │ │ ├── state.xml │ │ └── system.xml │ ├── trpzip2-explicit │ │ ├── README │ │ ├── trpzip2.crd │ │ └── trpzip2.prmtop │ └── waterbox │ │ ├── tip3p900.pdb │ │ ├── watbox216.crd │ │ ├── watbox216.pdb │ │ └── watbox216.prmtop ├── forcefactories.py ├── forces.py ├── integrators.py ├── mcmc.py ├── mit_license.txt ├── multistate │ ├── __init__.py │ ├── multistateanalyzer.py │ ├── multistatereporter.py │ ├── multistatesampler.py │ ├── paralleltempering.py │ ├── pymbar.py │ ├── replicaexchange.py │ ├── sams.py │ └── utils.py ├── respa.py ├── scripts │ ├── __init__.py │ └── test_openmm_platforms.py ├── sobol.py ├── states.py ├── storage │ ├── __init__.py │ ├── iodrivers.py │ └── storageinterface.py ├── tests │ ├── conftest.py │ ├── test_alchemy.py │ ├── test_cache.py │ ├── test_forcefactories.py │ ├── test_forces.py │ ├── test_integrators.py │ ├── test_integrators_and_testsystems.py │ ├── test_mcmc.py │ ├── test_mixing.py │ ├── test_platforms.py │ ├── test_sampling.py │ ├── test_states.py │ ├── test_storage_interface.py │ ├── test_storage_iodrivers.py │ ├── test_testsystems.py │ └── test_utils.py ├── testsystems.py └── utils │ ├── __init__.py │ ├── equilibration.py │ └── 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