setup.py
./Yank/mixing/_mix_replicas.c
Yank/__init__.py
Yank/analyze.py
Yank/cli.py
Yank/pipeline.py
Yank/repex.py
Yank/restraints.py
Yank/sampling.py
Yank/systembuilder.py
Yank/utils.py
Yank/version.py
Yank/yamlbuild.py
Yank/yank.py
Yank/../examples/README.md
Yank/../examples/abl-imatinib-explicit/README.md
Yank/../examples/abl-imatinib-explicit/render_trajectory.py
Yank/../examples/abl-imatinib-explicit/run-torque.sh
Yank/../examples/abl-imatinib-explicit/run.sh
Yank/../examples/abl-imatinib-explicit/visualize.tcsh
Yank/../examples/abl-imatinib-explicit/yank.yaml
Yank/../examples/abl-imatinib-explicit/input/2HYY-pdbfixer.pdb
Yank/../examples/abl-imatinib-explicit/input/2HYY.pdb
Yank/../examples/abl-imatinib-explicit/input/README.md
Yank/../examples/abl-imatinib-explicit/input/STI-extract.pdb
Yank/../examples/abl-imatinib-explicit/input/STI02.mol2
Yank/../examples/abl-imatinib-implicit/run-torque-extend.sh
Yank/../examples/abl-imatinib-implicit/run-torque.sh
Yank/../examples/abl-imatinib-implicit/run.sh
Yank/../examples/abl-imatinib-implicit/setup/2HYY-pdbfixer.pdb
Yank/../examples/abl-imatinib-implicit/setup/2HYY.pdb
Yank/../examples/abl-imatinib-implicit/setup/README.md
Yank/../examples/abl-imatinib-implicit/setup/STI-extract.pdb
Yank/../examples/abl-imatinib-implicit/setup/STI02.mol2
Yank/../examples/abl-imatinib-implicit/setup/complex.inpcrd
Yank/../examples/abl-imatinib-implicit/setup/complex.pdb
Yank/../examples/abl-imatinib-implicit/setup/complex.prmtop
Yank/../examples/abl-imatinib-implicit/setup/setup.leap.in
Yank/../examples/abl-imatinib-implicit/setup/setup.sh
Yank/../examples/abl-imatinib-implicit/setup/solvent.inpcrd
Yank/../examples/abl-imatinib-implicit/setup/solvent.pdb
Yank/../examples/abl-imatinib-implicit/setup/solvent.prmtop
Yank/../examples/abl-imatinib-implicit/setup/vacuum.inpcrd
Yank/../examples/abl-imatinib-implicit/setup/vacuum.pdb
Yank/../examples/abl-imatinib-implicit/setup/vacuum.prmtop
Yank/../examples/benzene-hydration-explicit/README.md
Yank/../examples/benzene-hydration-explicit/run-torque.sh
Yank/../examples/benzene-hydration-explicit/run.sh
Yank/../examples/benzene-hydration-explicit/yank.yaml
Yank/../examples/benzene-hydration-explicit/input/benzene.tripos.mol2
Yank/../examples/benzene-toluene-explicit/README.md
Yank/../examples/benzene-toluene-explicit/run.sh
Yank/../examples/benzene-toluene-explicit/setup/benzene.frcmod
Yank/../examples/benzene-toluene-explicit/setup/benzene.gaff.mol2
Yank/../examples/benzene-toluene-explicit/setup/benzene.tripos.mol2
Yank/../examples/benzene-toluene-explicit/setup/complex.inpcrd
Yank/../examples/benzene-toluene-explicit/setup/complex.pdb
Yank/../examples/benzene-toluene-explicit/setup/complex.prmtop
Yank/../examples/benzene-toluene-explicit/setup/generate-molecules.py
Yank/../examples/benzene-toluene-explicit/setup/receptor.prmtop
Yank/../examples/benzene-toluene-explicit/setup/setup.leap.in
Yank/../examples/benzene-toluene-explicit/setup/setup.sh
Yank/../examples/benzene-toluene-explicit/setup/solvent.inpcrd
Yank/../examples/benzene-toluene-explicit/setup/solvent.pdb
Yank/../examples/benzene-toluene-explicit/setup/solvent.prmtop
Yank/../examples/benzene-toluene-explicit/setup/toluene.frcmod
Yank/../examples/benzene-toluene-explicit/setup/toluene.gaff.mol2
Yank/../examples/benzene-toluene-explicit/setup/toluene.tripos.mol2
Yank/../examples/benzene-toluene-explicit/setup/vacuum.inpcrd
Yank/../examples/benzene-toluene-explicit/setup/vacuum.pdb
Yank/../examples/benzene-toluene-explicit/setup/vacuum.prmtop
Yank/../examples/benzene-toluene-implicit/README.md
Yank/../examples/benzene-toluene-implicit/run.sh
Yank/../examples/benzene-toluene-implicit/setup/benzene.frcmod
Yank/../examples/benzene-toluene-implicit/setup/benzene.gaff.mol2
Yank/../examples/benzene-toluene-implicit/setup/complex.inpcrd
Yank/../examples/benzene-toluene-implicit/setup/complex.pdb
Yank/../examples/benzene-toluene-implicit/setup/complex.prmtop
Yank/../examples/benzene-toluene-implicit/setup/generate-molecules.py
Yank/../examples/benzene-toluene-implicit/setup/receptor.inpcrd
Yank/../examples/benzene-toluene-implicit/setup/receptor.pdb
Yank/../examples/benzene-toluene-implicit/setup/receptor.prmtop
Yank/../examples/benzene-toluene-implicit/setup/setup.leap.in
Yank/../examples/benzene-toluene-implicit/setup/setup.sh
Yank/../examples/benzene-toluene-implicit/setup/solvent.inpcrd
Yank/../examples/benzene-toluene-implicit/setup/solvent.pdb
Yank/../examples/benzene-toluene-implicit/setup/solvent.prmtop
Yank/../examples/host-guest-explicit/run-torque.sh
Yank/../examples/host-guest-explicit/run.sh
Yank/../examples/host-guest-explicit/setup/complex.inpcrd
Yank/../examples/host-guest-explicit/setup/complex.pdb
Yank/../examples/host-guest-explicit/setup/complex.prmtop
Yank/../examples/host-guest-explicit/setup/generate-mol2-from-name.py
Yank/../examples/host-guest-explicit/setup/guest.tripos.mol2
Yank/../examples/host-guest-explicit/setup/host.tripos.mol2
Yank/../examples/host-guest-explicit/setup/leap.log
Yank/../examples/host-guest-explicit/setup/ligand.gaff.frcmod
Yank/../examples/host-guest-explicit/setup/ligand.gaff.mol2
Yank/../examples/host-guest-explicit/setup/ligand.tripos.mol2
Yank/../examples/host-guest-explicit/setup/receptor.gaff.frcmod
Yank/../examples/host-guest-explicit/setup/receptor.gaff.mol2
Yank/../examples/host-guest-explicit/setup/receptor.ligand.frcmod
Yank/../examples/host-guest-explicit/setup/receptor.ligand.mol2
Yank/../examples/host-guest-explicit/setup/setup.leap.in
Yank/../examples/host-guest-explicit/setup/setup.leap.out
Yank/../examples/host-guest-explicit/setup/setup.sh
Yank/../examples/host-guest-explicit/setup/solvent.inpcrd
Yank/../examples/host-guest-explicit/setup/solvent.pdb
Yank/../examples/host-guest-explicit/setup/solvent.prmtop
Yank/../examples/host-guest-explicit/setup/vacuum.inpcrd
Yank/../examples/host-guest-explicit/setup/vacuum.pdb
Yank/../examples/host-guest-explicit/setup/vacuum.prmtop
Yank/../examples/host-guest-implicit/README.md
Yank/../examples/host-guest-implicit/run-torque.sh
Yank/../examples/host-guest-implicit/run.sh
Yank/../examples/host-guest-implicit/setup/complex.inpcrd
Yank/../examples/host-guest-implicit/setup/complex.pdb
Yank/../examples/host-guest-implicit/setup/complex.prmtop
Yank/../examples/host-guest-implicit/setup/generate-mol2-from-name.py
Yank/../examples/host-guest-implicit/setup/guest.tripos.mol2
Yank/../examples/host-guest-implicit/setup/host.tripos.mol2
Yank/../examples/host-guest-implicit/setup/ligand.gaff.frcmod
Yank/../examples/host-guest-implicit/setup/ligand.gaff.mol2
Yank/../examples/host-guest-implicit/setup/ligand.tripos.mol2
Yank/../examples/host-guest-implicit/setup/receptor.gaff.frcmod
Yank/../examples/host-guest-implicit/setup/receptor.gaff.mol2
Yank/../examples/host-guest-implicit/setup/receptor.ligand.frcmod
Yank/../examples/host-guest-implicit/setup/receptor.ligand.mol2
Yank/../examples/host-guest-implicit/setup/setup.leap.in
Yank/../examples/host-guest-implicit/setup/setup.leap.out
Yank/../examples/host-guest-implicit/setup/setup.sh
Yank/../examples/host-guest-implicit/setup/solvent.inpcrd
Yank/../examples/host-guest-implicit/setup/solvent.pdb
Yank/../examples/host-guest-implicit/setup/solvent.prmtop
Yank/../examples/host-guest-implicit/setup/vacuum.inpcrd
Yank/../examples/host-guest-implicit/setup/vacuum.pdb
Yank/../examples/host-guest-implicit/setup/vacuum.prmtop
Yank/../examples/human-serum-albumin-explicit/README.md
Yank/../examples/human-serum-albumin-explicit/render_trajectory.py
Yank/../examples/human-serum-albumin-explicit/run-torque-extend.sh
Yank/../examples/human-serum-albumin-explicit/run-torque.sh
Yank/../examples/human-serum-albumin-explicit/run.sh
Yank/../examples/human-serum-albumin-explicit/visualize.tcsh
Yank/../examples/human-serum-albumin-explicit-yaml/README.md
Yank/../examples/human-serum-albumin-explicit-yaml/run-torque-extend.sh
Yank/../examples/human-serum-albumin-explicit-yaml/run-torque.sh
Yank/../examples/human-serum-albumin-explicit-yaml/run.sh
Yank/../examples/human-serum-albumin-explicit-yaml/yank.yaml
Yank/../examples/human-serum-albumin-explicit-yaml/structures/2I30.pdb
Yank/../examples/human-serum-albumin-explicit-yaml/structures/ANTECHAMBER_AC.AC
Yank/../examples/human-serum-albumin-explicit-yaml/structures/ANTECHAMBER_AC.AC0
Yank/../examples/human-serum-albumin-explicit-yaml/structures/ANTECHAMBER_AM1BCC.AC
Yank/../examples/human-serum-albumin-explicit-yaml/structures/ANTECHAMBER_AM1BCC_PRE.AC
Yank/../examples/human-serum-albumin-explicit-yaml/structures/ANTECHAMBER_BOND_TYPE.AC
Yank/../examples/human-serum-albumin-explicit-yaml/structures/ANTECHAMBER_BOND_TYPE.AC0
Yank/../examples/human-serum-albumin-explicit-yaml/structures/ATOMTYPE.INF
Yank/../examples/human-serum-albumin-explicit-yaml/structures/Lapatinib.mol2
Yank/../examples/human-serum-albumin-explicit-yaml/structures/README.md
Yank/../examples/human-serum-albumin-explicit-yaml/structures/cleanup.sh
Yank/../examples/human-serum-albumin-explicit-yaml/structures/clinical-kinase-inhibitors.csv
Yank/../examples/human-serum-albumin-explicit-yaml/structures/complex.inpcrd
Yank/../examples/human-serum-albumin-explicit-yaml/structures/complex.pdb
Yank/../examples/human-serum-albumin-explicit-yaml/structures/complex.prmtop
Yank/../examples/human-serum-albumin-explicit-yaml/structures/generate-mol2-from-name.py
Yank/../examples/human-serum-albumin-explicit-yaml/structures/leap.log
Yank/../examples/human-serum-albumin-explicit-yaml/structures/ligand.gaff.frcmod
Yank/../examples/human-serum-albumin-explicit-yaml/structures/ligand.gaff.mol2
Yank/../examples/human-serum-albumin-explicit-yaml/structures/ligand.tripos.mol2
Yank/../examples/human-serum-albumin-explicit-yaml/structures/receptor.pdbfixer.CYX.pdb
Yank/../examples/human-serum-albumin-explicit-yaml/structures/setup.leap.in
Yank/../examples/human-serum-albumin-explicit-yaml/structures/setup.leap.out
Yank/../examples/human-serum-albumin-explicit-yaml/structures/setup.sh
Yank/../examples/human-serum-albumin-explicit-yaml/structures/solvent.inpcrd
Yank/../examples/human-serum-albumin-explicit-yaml/structures/solvent.pdb
Yank/../examples/human-serum-albumin-explicit-yaml/structures/solvent.prmtop
Yank/../examples/human-serum-albumin-explicit-yaml/structures/sqm.in
Yank/../examples/human-serum-albumin-explicit-yaml/structures/sqm.out
Yank/../examples/human-serum-albumin-explicit-yaml/structures/sqm.pdb
Yank/../examples/human-serum-albumin-explicit-yaml/structures/vacuum.inpcrd
Yank/../examples/human-serum-albumin-explicit-yaml/structures/vacuum.pdb
Yank/../examples/human-serum-albumin-explicit-yaml/structures/vacuum.prmtop
Yank/../examples/human-serum-albumin-explicit/setup/2I30.pdb
Yank/../examples/human-serum-albumin-explicit/setup/ANTECHAMBER_AC.AC
Yank/../examples/human-serum-albumin-explicit/setup/ANTECHAMBER_AC.AC0
Yank/../examples/human-serum-albumin-explicit/setup/ANTECHAMBER_AM1BCC.AC
Yank/../examples/human-serum-albumin-explicit/setup/ANTECHAMBER_AM1BCC_PRE.AC
Yank/../examples/human-serum-albumin-explicit/setup/ANTECHAMBER_BOND_TYPE.AC
Yank/../examples/human-serum-albumin-explicit/setup/ANTECHAMBER_BOND_TYPE.AC0
Yank/../examples/human-serum-albumin-explicit/setup/ATOMTYPE.INF
Yank/../examples/human-serum-albumin-explicit/setup/README.md
Yank/../examples/human-serum-albumin-explicit/setup/cleanup.sh
Yank/../examples/human-serum-albumin-explicit/setup/complex.inpcrd
Yank/../examples/human-serum-albumin-explicit/setup/complex.pdb
Yank/../examples/human-serum-albumin-explicit/setup/complex.prmtop
Yank/../examples/human-serum-albumin-explicit/setup/generate-mol2-from-name.py
Yank/../examples/human-serum-albumin-explicit/setup/leap.log
Yank/../examples/human-serum-albumin-explicit/setup/ligand.gaff.frcmod
Yank/../examples/human-serum-albumin-explicit/setup/ligand.gaff.mol2
Yank/../examples/human-serum-albumin-explicit/setup/ligand.tripos.mol2
Yank/../examples/human-serum-albumin-explicit/setup/receptor.pdbfixer.CYX.pdb
Yank/../examples/human-serum-albumin-explicit/setup/setup.leap.in
Yank/../examples/human-serum-albumin-explicit/setup/setup.leap.out
Yank/../examples/human-serum-albumin-explicit/setup/setup.sh
Yank/../examples/human-serum-albumin-explicit/setup/solvent.inpcrd
Yank/../examples/human-serum-albumin-explicit/setup/solvent.pdb
Yank/../examples/human-serum-albumin-explicit/setup/solvent.prmtop
Yank/../examples/human-serum-albumin-explicit/setup/sqm.in
Yank/../examples/human-serum-albumin-explicit/setup/sqm.out
Yank/../examples/human-serum-albumin-explicit/setup/sqm.pdb
Yank/../examples/human-serum-albumin-explicit/setup/vacuum.inpcrd
Yank/../examples/human-serum-albumin-explicit/setup/vacuum.pdb
Yank/../examples/human-serum-albumin-explicit/setup/vacuum.prmtop
Yank/../examples/human-serum-albumin-implicit/README.md
Yank/../examples/human-serum-albumin-implicit/render_trajectory.py
Yank/../examples/human-serum-albumin-implicit/run-torque.sh
Yank/../examples/human-serum-albumin-implicit/run.sh
Yank/../examples/human-serum-albumin-implicit/visualize.tcsh
Yank/../examples/human-serum-albumin-implicit/setup/2I2Z.pdb
Yank/../examples/human-serum-albumin-implicit/setup/cleanup.sh
Yank/../examples/human-serum-albumin-implicit/setup/complex.inpcrd
Yank/../examples/human-serum-albumin-implicit/setup/complex.pdb
Yank/../examples/human-serum-albumin-implicit/setup/complex.prmtop
Yank/../examples/human-serum-albumin-implicit/setup/generate-mol2-from-name.py
Yank/../examples/human-serum-albumin-implicit/setup/leap.log
Yank/../examples/human-serum-albumin-implicit/setup/receptor.pdbfixer.CYX.pdb
Yank/../examples/human-serum-albumin-implicit/setup/receptor.pdbfixer.pdb
Yank/../examples/human-serum-albumin-implicit/setup/setup.leap.in
Yank/../examples/human-serum-albumin-implicit/setup/setup.leap.out
Yank/../examples/human-serum-albumin-implicit/setup/setup.sh
Yank/../examples/human-serum-albumin-implicit/setup/solvent.inpcrd
Yank/../examples/human-serum-albumin-implicit/setup/solvent.pdb
Yank/../examples/human-serum-albumin-implicit/setup/solvent.prmtop
Yank/../examples/human-serum-albumin-implicit/setup/vacuum.inpcrd
Yank/../examples/human-serum-albumin-implicit/setup/vacuum.pdb
Yank/../examples/human-serum-albumin-implicit/setup/vacuum.prmtop
Yank/../examples/hydration-smiles/README.md
Yank/../examples/hydration-smiles/freesolv-mini.smiles
Yank/../examples/hydration-smiles/freesolv.yaml
Yank/../examples/hydration-smiles/run-torque.sh
Yank/../examples/mhc-peptide-tcr/mhc-peptide-tcr.py
Yank/../examples/mhc-peptide-tcr/render_trajectory.py
Yank/../examples/mhc-peptide-tcr/run-torque.sh
Yank/../examples/mhc-peptide-tcr/run.sh
Yank/../examples/mhc-peptide-tcr/visualize.tcsh
Yank/../examples/p-xylene-explicit/README.md
Yank/../examples/p-xylene-explicit/run-torque-extend.sh
Yank/../examples/p-xylene-explicit/run-torque.sh
Yank/../examples/p-xylene-explicit/run.sh
Yank/../examples/p-xylene-explicit/yank.yaml
Yank/../examples/p-xylene-explicit/setup/181L.pdb
Yank/../examples/p-xylene-explicit/setup/187L.pdb
Yank/../examples/p-xylene-explicit/setup/README.md
Yank/../examples/p-xylene-explicit/setup/complex.inpcrd
Yank/../examples/p-xylene-explicit/setup/complex.pdb
Yank/../examples/p-xylene-explicit/setup/complex.prmtop
Yank/../examples/p-xylene-explicit/setup/generate-mol2-from-name.py
Yank/../examples/p-xylene-explicit/setup/leap.log
Yank/../examples/p-xylene-explicit/setup/ligand.frcmod
Yank/../examples/p-xylene-explicit/setup/ligand.gaff.frcmod
Yank/../examples/p-xylene-explicit/setup/ligand.gaff.mol2
Yank/../examples/p-xylene-explicit/setup/ligand.tripos.mol2
Yank/../examples/p-xylene-explicit/setup/receptor.pdbfixer.pdb
Yank/../examples/p-xylene-explicit/setup/setup.leap.in
Yank/../examples/p-xylene-explicit/setup/setup.sh
Yank/../examples/p-xylene-explicit/setup/solvent.inpcrd
Yank/../examples/p-xylene-explicit/setup/solvent.pdb
Yank/../examples/p-xylene-explicit/setup/solvent.prmtop
Yank/../examples/p-xylene-explicit/setup/sqm.pdb
Yank/../examples/p-xylene-explicit/setup/vacuum.inpcrd
Yank/../examples/p-xylene-explicit/setup/vacuum.pdb
Yank/../examples/p-xylene-explicit/setup/vacuum.prmtop
Yank/../examples/p-xylene-gromacs-example/README.md
Yank/../examples/p-xylene-gromacs-example/run-torque.sh
Yank/../examples/p-xylene-gromacs-example/run.sh
Yank/../examples/p-xylene-gromacs-example/setup/README.md
Yank/../examples/p-xylene-gromacs-example/setup/complex.gro
Yank/../examples/p-xylene-gromacs-example/setup/complex.top
Yank/../examples/p-xylene-gromacs-example/setup/simulateGromacs.py
Yank/../examples/p-xylene-gromacs-example/setup/solvent.gro
Yank/../examples/p-xylene-gromacs-example/setup/solvent.top
Yank/../examples/p-xylene-gromacs-example/setup/top/p-xyle.itp
Yank/../examples/p-xylene-gromacs-example/setup/top/charmm36.ff/atomtypes.atp
Yank/../examples/p-xylene-gromacs-example/setup/top/charmm36.ff/cmap.itp
Yank/../examples/p-xylene-gromacs-example/setup/top/charmm36.ff/ffbonded.itp
Yank/../examples/p-xylene-gromacs-example/setup/top/charmm36.ff/ffnonbonded.itp
Yank/../examples/p-xylene-gromacs-example/setup/top/charmm36.ff/forcefield.doc
Yank/../examples/p-xylene-gromacs-example/setup/top/charmm36.ff/forcefield.itp
Yank/../examples/p-xylene-gromacs-example/setup/top/charmm36.ff/gb.itp
Yank/../examples/p-xylene-gromacs-example/setup/top/charmm36.ff/ions.itp
Yank/../examples/p-xylene-gromacs-example/setup/top/charmm36.ff/merged.arn
Yank/../examples/p-xylene-gromacs-example/setup/top/charmm36.ff/merged.c.tdb
Yank/../examples/p-xylene-gromacs-example/setup/top/charmm36.ff/merged.hdb
Yank/../examples/p-xylene-gromacs-example/setup/top/charmm36.ff/merged.n.tdb
Yank/../examples/p-xylene-gromacs-example/setup/top/charmm36.ff/merged.r2b
Yank/../examples/p-xylene-gromacs-example/setup/top/charmm36.ff/merged.rtp
Yank/../examples/p-xylene-gromacs-example/setup/top/charmm36.ff/merged.vsd
Yank/../examples/p-xylene-gromacs-example/setup/top/charmm36.ff/nbfix.itp
Yank/../examples/p-xylene-gromacs-example/setup/top/charmm36.ff/spc.itp
Yank/../examples/p-xylene-gromacs-example/setup/top/charmm36.ff/spce.itp
Yank/../examples/p-xylene-gromacs-example/setup/top/charmm36.ff/tip3p.itp
Yank/../examples/p-xylene-gromacs-example/setup/top/charmm36.ff/tip4p.itp
Yank/../examples/p-xylene-gromacs-example/setup/top/charmm36.ff/watermodels.dat
Yank/../examples/p-xylene-implicit/README.md
Yank/../examples/p-xylene-implicit/run-torque.sh
Yank/../examples/p-xylene-implicit/run.sh
Yank/../examples/p-xylene-implicit/yank.yaml
Yank/../examples/p-xylene-implicit/input/181L-pdbfixer.pdb
Yank/../examples/p-xylene-implicit/input/p-xylene.mol2
Yank/../examples/s-alpha-ionone-explicit/README.md
Yank/../examples/s-alpha-ionone-explicit/run-torque.sh
Yank/../examples/s-alpha-ionone-explicit/run.sh
Yank/../examples/s-alpha-ionone-explicit/setup/CYP_IC6.off
Yank/../examples/s-alpha-ionone-explicit/setup/HEME_IC6.off
Yank/../examples/s-alpha-ionone-explicit/setup/IC6.frcmod
Yank/../examples/s-alpha-ionone-explicit/setup/complex.inpcrd
Yank/../examples/s-alpha-ionone-explicit/setup/complex.pdb
Yank/../examples/s-alpha-ionone-explicit/setup/complex.prmtop
Yank/../examples/s-alpha-ionone-explicit/setup/em.mdp
Yank/../examples/s-alpha-ionone-explicit/setup/leap.conf
Yank/../examples/s-alpha-ionone-explicit/setup/leap.in
Yank/../examples/s-alpha-ionone-explicit/setup/leap.log
Yank/../examples/s-alpha-ionone-explicit/setup/md.mdp
Yank/../examples/s-alpha-ionone-explicit/setup/ranked_S-alpha-ionone_m1_13.2.pdb
Yank/../examples/s-alpha-ionone-explicit/setup/receptor.inpcrd
Yank/../examples/s-alpha-ionone-explicit/setup/receptor.pdb
Yank/../examples/s-alpha-ionone-explicit/setup/receptor.prmtop
Yank/../examples/s-alpha-ionone-explicit/setup/s-a-ion.prepin
Yank/../examples/s-alpha-ionone-explicit/setup/s-a-ion.prepin.bu
Yank/../examples/s-alpha-ionone-explicit/setup/solvent.inpcrd
Yank/../examples/s-alpha-ionone-explicit/setup/solvent.pdb
Yank/../examples/s-alpha-ionone-explicit/setup/solvent.prmtop
Yank/../examples/s-alpha-ionone-explicit/setup/testout.pdb
Yank/../examples/tip3p-in-tip3p/README.md
Yank/../examples/tip3p-in-tip3p/run-torque.sh
Yank/../examples/tip3p-in-tip3p/run.sh
Yank/../examples/tip3p-in-tip3p/yank.yaml
Yank/../examples/tip3p-in-tip3p/input/tip3p-molecule.mol2
Yank/../examples/yank-yaml-cookbook/README.md
Yank/../examples/yank-yaml-cookbook/all-options.yaml
Yank/../examples/yank-yaml-cookbook/combinatorial-experiment.yaml
Yank/commands/__init__.py
Yank/commands/analyze.py
Yank/commands/cite.py
Yank/commands/cleanup.py
Yank/commands/help.py
Yank/commands/platforms.py
Yank/commands/prepare.py
Yank/commands/run.py
Yank/commands/script.py
Yank/commands/selftest.py
Yank/commands/status.py
Yank/mixing/__init__.py
Yank/mixing/_mix_replicas_old.py
Yank/tests/__init__.py
Yank/tests/test_cli.py
Yank/tests/test_commands.py
Yank/tests/test_examples.py
Yank/tests/test_mixing.py
Yank/tests/test_prepare.py
Yank/tests/test_repex.py
Yank/tests/test_utils.py
Yank/tests/test_yaml.py
Yank/tests/test_yank.py
yank.egg-info/PKG-INFO
yank.egg-info/SOURCES.txt
yank.egg-info/dependency_links.txt
yank.egg-info/entry_points.txt
yank.egg-info/not-zip-safe
yank.egg-info/requires.txt
yank.egg-info/top_level.txt