MANIFEST.in
README.txt
setup.cfg
setup.py
bin/ForceBalance
bin/ForceBalance.py
bin/MakeInputFile.py
bin/TidyOutput
bin/filecnv.py
doc/DoxygenLayout.xml
doc/ForceBalance-Manual.pdf
doc/add-tabs.py
doc/doxygen.cfg
doc/doxypy.py
doc/glossary.txt
doc/header.tex
doc/installation.txt
doc/introduction.txt
doc/make-option-index.py
doc/makedocumentation.py
doc/roadmap.txt
doc/tutorial.txt
doc/usage.txt
doc/Images/ForceBalance.pdf
doc/Images/ForceBalanceLogo_sm.png
doc/Images/convert-images.txt
doc/Images/cycle.png
doc/Images/cycle_sm.png
doc/Images/flowchart.png
doc/Images/flowchart_sm.png
doc/Images/interactions.png
doc/Images/interactions_sm.png
doc/Images/ladder.png
doc/Images/ladder_sm.png
doc/callgraph/CallGraph.py
doc/callgraph/Run_To_Make_Cool_Picture.sh
ext/molfile_plugin/LICENSE
ext/molfile_plugin/Makefile
ext/molfile_plugin/dcdplugin.c
ext/molfile_plugin/dcdplugin_s.c
ext/molfile_plugin/endianswap.h
ext/molfile_plugin/fastio.h
ext/molfile_plugin/largefiles.h
ext/molfile_plugin/namdbinplugin.c
ext/molfile_plugin/include/import_graphics_plugin.h
ext/molfile_plugin/include/molfile_plugin.h
ext/molfile_plugin/include/vmdconio.h
ext/molfile_plugin/include/vmdplugin.h
forcebalance.egg-info/PKG-INFO
forcebalance.egg-info/SOURCES.txt
forcebalance.egg-info/dependency_links.txt
forcebalance.egg-info/top_level.txt
src/AUTHORS
src/Mol2.py
src/PDB.py
src/PT.py
src/__init__.py
src/abinitio.py
src/abinitio_internal.py
src/amberio.py
src/binding.py
src/chemistry.py
src/contact.py
src/counterpoise.py
src/custom_io.py
src/engine.py
src/finite_difference.py
src/forcefield.py
src/gmxio.py
src/hydration.py
src/interaction.py
src/leastsq.py
src/lipid.py
src/liquid.py
src/molecule.py
src/moments.py
src/nifty.py
src/objective.py
src/openmmio.py
src/optimizer.py
src/output.py
src/parser.py
src/psi4io.py
src/qchemio.py
src/quantity.py
src/readfrq.py
src/target.py
src/thermo.py
src/tinkerio.py
src/vibration.py
src/data/data.csv.template
src/data/gmxprefix.bash
src/data/md_chain.py
src/data/md_ism_hfe.py
src/data/npt.py
src/data/npt_lipid.py
src/data/nvt.py
src/data/rtarget.py
src/data/run_psi_rdvr3_objective.sh
src/data/runamber.sh
src/data/runcuda.sh
src/data/rungmx.sh
src/data/runtinker.sh
src/gui/About.txt
src/gui/__init__.py
src/gui/__main__.py
src/gui/app.py
src/gui/elements.py
src/gui/objects.py
src/legacy/abinitio.py
src/unit/__init__.py
src/unit/basedimension.py
src/unit/baseunit.py
src/unit/constants.py
src/unit/doctests.py
src/unit/mymatrix.py
src/unit/prefix.py
src/unit/quantity.py
src/unit/standard_dimensions.py
src/unit/unit.py
src/unit/unit_definitions.py
src/unit/unit_math.py
src/unit/unit_operators.py
studies/001_water_tutorial/0.energy_force.in
studies/001_water_tutorial/1.netforce_torque.in
studies/001_water_tutorial/2.L1_penalty.in
studies/001_water_tutorial/3.no_penalty.in
studies/001_water_tutorial/4.change_factor.in
studies/001_water_tutorial/5.gradient.in
studies/001_water_tutorial/calibrate.in
studies/001_water_tutorial/newpriors.in
studies/001_water_tutorial/targets.tar.bz2
studies/001_water_tutorial/validate.in
studies/001_water_tutorial/very_simple.in
studies/001_water_tutorial/very_simple_remote.in
studies/001_water_tutorial/continue/very_simple.err
studies/001_water_tutorial/continue/very_simple.out
studies/001_water_tutorial/continue/very_simple.sav
studies/001_water_tutorial/continue/very_simple_2.out
studies/001_water_tutorial/forcefield/water.itp
studies/002_Mar13_OpenMM_Workshop/ForceBalance_DMS_Tutorial.docx
studies/002_Mar13_OpenMM_Workshop/ForceBalance_DMS_Tutorial.pdf
studies/002_Mar13_OpenMM_Workshop/Setup.tar.bz2
studies/002_Mar13_OpenMM_Workshop/optimize-qm.in
studies/002_Mar13_OpenMM_Workshop/optimize-simple.in
studies/002_Mar13_OpenMM_Workshop/targets.tar.bz2
studies/002_Mar13_OpenMM_Workshop/forcefield/dms.xml
studies/002_Mar13_OpenMM_Workshop/illustrations/ansi2html.sh
studies/002_Mar13_OpenMM_Workshop/illustrations/energies.pdf
studies/002_Mar13_OpenMM_Workshop/illustrations/optimize-qm.dat
studies/002_Mar13_OpenMM_Workshop/illustrations/plot-energies.gp
studies/003_liquid_bromine/optimize.in
studies/003_liquid_bromine/single-wq.in
studies/003_liquid_bromine/single.in
studies/003_liquid_bromine/forcefield/about.txt
studies/003_liquid_bromine/forcefield/bro.itp
studies/003_liquid_bromine/forcefield/bro.orig.itp
studies/003_liquid_bromine/targets/LiquidBromine/data.csv
studies/003_liquid_bromine/targets/LiquidBromine/gas.gro
studies/003_liquid_bromine/targets/LiquidBromine/gas.mdp
studies/003_liquid_bromine/targets/LiquidBromine/gas.top
studies/003_liquid_bromine/targets/LiquidBromine/liquid.gro
studies/003_liquid_bromine/targets/LiquidBromine/liquid.mdp
studies/003_liquid_bromine/targets/LiquidBromine/liquid.top
studies/003b_tinker_liquid_bromine/optimize.in
studies/003b_tinker_liquid_bromine/forcefield/bro.prm
studies/003b_tinker_liquid_bromine/targets/LiquidBromine/data.csv
studies/003b_tinker_liquid_bromine/targets/LiquidBromine/gas.key
studies/003b_tinker_liquid_bromine/targets/LiquidBromine/gas.xyz
studies/003b_tinker_liquid_bromine/targets/LiquidBromine/liquid.key
studies/003b_tinker_liquid_bromine/targets/LiquidBromine/liquid.xyz
studies/004_thermo_liquid_bromine/optimize.in
studies/004_thermo_liquid_bromine/single.in
studies/004_thermo_liquid_bromine/forcefield/about.txt
studies/004_thermo_liquid_bromine/forcefield/bro.itp
studies/004_thermo_liquid_bromine/forcefield/bro.orig.itp
studies/004_thermo_liquid_bromine/targets/LiquidBromine/about.txt
studies/004_thermo_liquid_bromine/targets/LiquidBromine/data.csv
studies/004_thermo_liquid_bromine/targets/LiquidBromine/expset.txt
studies/004_thermo_liquid_bromine/targets/LiquidBromine/1/sim1.gro
studies/004_thermo_liquid_bromine/targets/LiquidBromine/1/sim1.mdp
studies/004_thermo_liquid_bromine/targets/LiquidBromine/1/sim1.top
studies/004_thermo_liquid_bromine/targets/LiquidBromine/1/sim2.gro
studies/004_thermo_liquid_bromine/targets/LiquidBromine/1/sim2.mdp
studies/004_thermo_liquid_bromine/targets/LiquidBromine/1/sim2.top
studies/005_iamoeba/single-0.5fs.in
studies/005_iamoeba/single-0.5fs.out
studies/005_iamoeba/targets.tar.bz2
studies/005_iamoeba/forcefield/amoebawater.xml
studies/005_iamoeba/forcefield/water.prm
studies/005_iamoeba/result/amoebawater.xml
studies/005_iamoeba/result/water.prm
studies/006_ccl4_amoeba/ansi2html.sh
studies/006_ccl4_amoeba/optimize.in
studies/006_ccl4_amoeba/optimize.out
studies/006_ccl4_amoeba/forcefield/cl4.prm
studies/006_ccl4_amoeba/result/cl4.prm
studies/006_ccl4_amoeba/targets/ccl4-h2o-ix/all.arc
studies/006_ccl4_amoeba/targets/ccl4-h2o-ix/qdata.txt
studies/006_ccl4_amoeba/targets/ccl4-h2o-ix/shot.key
studies/006_ccl4_amoeba/targets/ccl4-liquid/data.csv
studies/006_ccl4_amoeba/targets/ccl4-liquid/gas.key
studies/006_ccl4_amoeba/targets/ccl4-liquid/gas.xyz
studies/006_ccl4_amoeba/targets/ccl4-liquid/liquid.key
studies/006_ccl4_amoeba/targets/ccl4-liquid/liquid.xyz
studies/007_tip4p_STP/optimize.in
studies/007_tip4p_STP/single.in
studies/007_tip4p_STP/single.out
studies/007_tip4p_STP/forcefield/tip4p.itp
studies/007_tip4p_STP/targets/Liquid/data.csv
studies/007_tip4p_STP/targets/Liquid/gas.gro
studies/007_tip4p_STP/targets/Liquid/gas.mdp
studies/007_tip4p_STP/targets/Liquid/gas.top
studies/007_tip4p_STP/targets/Liquid/liquid.gro
studies/007_tip4p_STP/targets/Liquid/liquid.mdp
studies/007_tip4p_STP/targets/Liquid/liquid.top
studies/007_tip4p_STP/targets/cluster-06/all.gro
studies/007_tip4p_STP/targets/cluster-06/qdata.txt
studies/007_tip4p_STP/targets/cluster-06/shot.mdp
studies/007_tip4p_STP/targets/cluster-06/topol.top
studies/008_thcdf/L1.1e-2.in
studies/008_thcdf/bh3-log-barrier.2.in
studies/008_thcdf/bh3-log-barrier.in
studies/008_thcdf/small.in
studies/008_thcdf/targets.tar.bz2
studies/008_thcdf/forcefield/cc-pvdz-overlap-original.gbs
studies/008_thcdf/forcefield/cc-pvdz-overlap.gbs
studies/008_thcdf/forcefield/throwout.dat
studies/009_voelz_nspe/About.txt
studies/009_voelz_nspe/Setup.tar.bz2
studies/009_voelz_nspe/options.in
studies/009_voelz_nspe/Nspe_2/About.txt
studies/009_voelz_nspe/Nspe_2/About_VAV.txt
studies/009_voelz_nspe/Nspe_2/Setup.tar.bz2
studies/009_voelz_nspe/Nspe_2/energies.dat
studies/009_voelz_nspe/Nspe_2/energies_Hartree.out
studies/009_voelz_nspe/Nspe_2/energies_kcalperMol.out
studies/009_voelz_nspe/Nspe_2/image_Nspe2.png
studies/009_voelz_nspe/Nspe_2/newton.in
studies/009_voelz_nspe/Nspe_2/newton.out
studies/009_voelz_nspe/Nspe_2/plot_phi_vs_chi.py
studies/009_voelz_nspe/Nspe_2/forcefield/molecule-dihedralbk.itp
studies/009_voelz_nspe/Nspe_2/forcefield/molecule.itp
studies/009_voelz_nspe/Nspe_2/forcefield/molecule0.itp
studies/009_voelz_nspe/Nspe_2/targets/nspe_2dscan/all.gro
studies/009_voelz_nspe/Nspe_2/targets/nspe_2dscan/qdata.txt
studies/009_voelz_nspe/Nspe_2/targets/nspe_2dscan/shot.mdp
studies/009_voelz_nspe/Nspe_2/targets/nspe_2dscan/topol.top
studies/009_voelz_nspe/analysis/2D-before-after.png
studies/009_voelz_nspe/analysis/after.top
studies/009_voelz_nspe/analysis/after.tpr
studies/009_voelz_nspe/analysis/all.gro
studies/009_voelz_nspe/analysis/before.tpr
studies/009_voelz_nspe/analysis/calc_singlepoints
studies/009_voelz_nspe/analysis/chi0.omega0.gro
studies/009_voelz_nspe/analysis/chi330.omega165.gro
studies/009_voelz_nspe/analysis/compare_before_after.py
studies/009_voelz_nspe/analysis/dihedral_plot.py
studies/009_voelz_nspe/analysis/ener.edr
studies/009_voelz_nspe/analysis/energy.xvg
studies/009_voelz_nspe/analysis/md.log
studies/009_voelz_nspe/analysis/mdout.mdp
studies/009_voelz_nspe/analysis/molecule_after-take1.itp
studies/009_voelz_nspe/analysis/molecule_after.itp
studies/009_voelz_nspe/analysis/peptoid1_VAV.xlsx
studies/009_voelz_nspe/analysis/singlepoint.mdp
studies/009_voelz_nspe/analysis/traj.trr
studies/009_voelz_nspe/forcefield/bondangdih.itp
studies/009_voelz_nspe/forcefield/dih.itp
studies/009_voelz_nspe/forcefield/dihang.itp
studies/009_voelz_nspe/forcefield/molecule.itp
studies/009_voelz_nspe/targets/2dscan/all.gro
studies/009_voelz_nspe/targets/2dscan/qdata.txt
studies/009_voelz_nspe/targets/2dscan/shot.mdp
studies/009_voelz_nspe/targets/2dscan/topol.top
studies/010_lipid_study/simple.in
studies/010_lipid_study/single.in
studies/010_lipid_study/forcefield/DPPC.itp
studies/010_lipid_study/forcefield/sigeps.txt
studies/010_lipid_study/targets/LipidDPPC/data.csv
studies/010_lipid_study/targets/LipidDPPC/lipid.gro
studies/010_lipid_study/targets/LipidDPPC/lipid.mdp
studies/010_lipid_study/targets/LipidDPPC/lipid.top
studies/010_lipid_study/targets/LipidDPPC/IC/323.15K-1.0atm/lipid.gro
studies/012_implicit_solvent_hfe/optimize.in
studies/012_implicit_solvent_hfe/forcefield/ethanol.xml
studies/012_implicit_solvent_hfe/targets/ethanol/hfedata.txt
studies/012_implicit_solvent_hfe/targets/ethanol/molecules/ethanol.pdb
studies/013_ammonia/newpriors.in
studies/013_ammonia/newpriors.out
studies/013_ammonia/oldpriors.in
studies/013_ammonia/oldpriors.out
studies/013_ammonia/precondition1.in
studies/013_ammonia/precondition1.out
studies/013_ammonia/forcefield/ammonia.itp
studies/013_ammonia/targets/Liquid/data.csv
studies/013_ammonia/targets/Liquid/gas.gro
studies/013_ammonia/targets/Liquid/gas.mdp
studies/013_ammonia/targets/Liquid/gas.top
studies/013_ammonia/targets/Liquid/liquid.gro
studies/013_ammonia/targets/Liquid/liquid.mdp
studies/013_ammonia/targets/Liquid/liquid.top
studies/014_chromophore/optimize.in
studies/014_chromophore/precondition.in
studies/014_chromophore/forcefield/res.frcmod
studies/014_chromophore/forcefield/res.mol2
studies/014_chromophore/forcefield/res.mol2.bak
studies/014_chromophore/forcefield/res1.mol2
studies/014_chromophore/forcefield/NewFF/res.frcmod
studies/014_chromophore/forcefield/NewFF/res.mol2
studies/014_chromophore/targets/AbInitio/all.gro
studies/014_chromophore/targets/AbInitio/all.mdcrd
studies/014_chromophore/targets/AbInitio/chromo.pdb
studies/014_chromophore/targets/AbInitio/qdata.txt
studies/014_chromophore/targets/AbInitio/stage.leap
studies/015_amoeba_tinker/example.in
studies/015_amoeba_tinker/targets.tar.bz2
studies/015_amoeba_tinker/forcefield/water.prm
studies/016_amber_fb15/About.txt
test/About.txt
test/__init__.py
test/__main__.py
test/__test__.py
test/test_continue.py
test/test_engine.py
test/test_finite_difference.py
test/test_forcefield.py
test/test_gmxio.py
test/test_molecule.py
test/test_nifty.py
test/test_objective.py
test/test_openmmio.py
test/test_optimizer.py
test/test_parser.py
test/test_system.py
test/test_target.py
test/test_tinkerio.py
test/files/0.energy_force.in
test/files/1.netforce_torque.in
test/files/ala.gro
test/files/dms_conf.pdb
test/files/lipid.gro
test/files/test_continue.in
test/files/test_continue.sav
test/files/very_simple.in
test/files/waterbox500.pdb
test/files/work_queue_worker
test/files/XmlScript_out/TIP3G2w_out_ref.xml
test/files/XmlScript_out/mvals.txt
test/files/amber_alaglu/AceAlaNme.itp
test/files/amber_alaglu/AceGluNme.itp
test/files/amber_alaglu/a99sb.itp
test/files/amber_alaglu/a99sb.prm
test/files/amber_alaglu/a99sb.xml
test/files/amber_alaglu/all.arc
test/files/amber_alaglu/all.gro
test/files/amber_alaglu/gro-vs-tinker.txt
test/files/amber_alaglu/shot.mdp
test/files/amber_alaglu/topol.top
test/files/amoeba_h2o6/amoebawater.xml
test/files/amoeba_h2o6/hex.arc
test/files/amoeba_h2o6/prism.key
test/files/amoeba_h2o6/prism.pdb
test/files/amoeba_h2o6/water.prm
test/files/forcefield/TIP3G2w.xml
test/files/forcefield/bro.itp
test/files/forcefield/cc-pvdz-overlap-original.gbs
test/files/forcefield/cl4.prm
test/files/forcefield/dms.xml
test/files/forcefield/water.itp
test/files/targets/About.txt
test/files/targets/make-settings.sh
test/files/targets/modify-gro.py
test/files/targets/shot.mdp
test/files/targets/LiquidBromine/data.csv
test/files/targets/LiquidBromine/gas.gro
test/files/targets/LiquidBromine/gas.mdp
test/files/targets/LiquidBromine/gas.top
test/files/targets/LiquidBromine/liquid.gro
test/files/targets/LiquidBromine/liquid.mdp
test/files/targets/LiquidBromine/liquid.top
test/files/targets/S2EPose/all.pdb
test/files/targets/S2EPose/qdata.txt
test/files/targets/ccl4-h2o-1/all.arc
test/files/targets/ccl4-h2o-1/qdata.txt
test/files/targets/ccl4-h2o-1/shot.key
test/files/targets/ccl4-h2o-2/all.arc
test/files/targets/ccl4-h2o-2/qdata.txt
test/files/targets/ccl4-h2o-2/shot.key
test/files/targets/ccpvdz/cc-pvdz-overlap.gbs
test/files/targets/ccpvdz/initial.dat
test/files/targets/ccpvdz/input.dat
test/files/targets/cluster-02/all.gro
test/files/targets/cluster-02/qdata.txt
test/files/targets/cluster-02/shot.mdp
test/files/targets/cluster-02/topol.top
test/files/targets/cluster-06/all.gro
test/files/targets/cluster-06/qdata.txt
test/files/targets/cluster-06/shot.mdp
test/files/targets/cluster-06/topol.top
test/files/targets/cluster-12/all.gro
test/files/targets/cluster-12/qdata.txt
test/files/targets/cluster-12/shot.mdp
test/files/targets/cluster-12/topol.top
test/files/targets/dms-liquid/data.csv
test/files/targets/dms-liquid/gas.pdb
test/files/targets/dms-liquid/liquid.pdb
test/files/targets/dms-liquid/runcuda.sh
test/files/targets/water12_fourpt/all.gro
test/files/targets/water12_fourpt/qdata.txt
test/files/test_continue.tmp/cluster-06/iter_0000/indicate.log
test/files/test_continue.tmp/cluster-06/iter_0000/mvals.txt
test/files/test_continue.tmp/cluster-06/iter_0000/objective.p
test/files/test_continue.tmp/cluster-06/iter_0000/water.itp
test/files/test_continue.tmp/cluster-06/iter_0001/indicate.log
test/files/test_continue.tmp/cluster-06/iter_0001/mvals.txt
test/files/test_continue.tmp/cluster-06/iter_0001/objective.p
test/files/test_continue.tmp/cluster-06/iter_0001/water.itp
test/files/test_continue.tmp/cluster-06/iter_0002/indicate.log
test/files/test_continue.tmp/cluster-06/iter_0002/mvals.txt
test/files/test_continue.tmp/cluster-06/iter_0002/objective.p
test/files/test_continue.tmp/cluster-06/iter_0002/water.itp
test/files/test_continue.tmp/cluster-12/iter_0000/indicate.log
test/files/test_continue.tmp/cluster-12/iter_0000/mvals.txt
test/files/test_continue.tmp/cluster-12/iter_0000/objective.p
test/files/test_continue.tmp/cluster-12/iter_0000/water.itp
test/files/test_continue.tmp/cluster-12/iter_0001/indicate.log
test/files/test_continue.tmp/cluster-12/iter_0001/mvals.txt
test/files/test_continue.tmp/cluster-12/iter_0001/objective.p
test/files/test_continue.tmp/cluster-12/iter_0001/water.itp
test/files/test_continue.tmp/cluster-12/iter_0002/indicate.log
test/files/test_continue.tmp/cluster-12/iter_0002/mvals.txt
test/files/test_continue.tmp/cluster-12/iter_0002/objective.p
test/files/test_continue.tmp/cluster-12/iter_0002/water.itp
test/files/test_engine/TestAmber99SB/test_energy_force.dat
test/files/test_engine/TestAmber99SB/test_interaction_energies.dat
test/files/test_engine/TestAmber99SB/test_multipole_moments.dipole.dat
test/files/test_engine/TestAmber99SB/test_multipole_moments.quadrupole.dat
test/files/test_engine/TestAmber99SB/test_multipole_moments_optimized.dipole.dat
test/files/test_engine/TestAmber99SB/test_multipole_moments_optimized.quadrupole.dat
test/files/test_engine/TestAmber99SB/test_normal_modes.freq.dat
test/files/test_engine/TestAmber99SB/test_normal_modes.mode.dat.npy
test/files/test_engine/TestAmber99SB/test_normal_modes_optimized.freq.dat
test/files/test_engine/TestAmber99SB/test_normal_modes_optimized.mode.dat.npy
test/files/test_engine/TestAmber99SB/test_optimized_geometries.dat
test/files/test_engine/TestAmoebaWater6/test_energy_force.dat
test/files/test_engine/TestAmoebaWater6/test_interaction_energy.dat
test/files/test_engine/TestAmoebaWater6/test_multipole_moments.dipole.dat
test/files/test_engine/TestAmoebaWater6/test_multipole_moments.quadrupole.dat
tools/About.txt
tools/Augment.py
tools/CallMSMS.py
tools/Condense_Interactions.py
tools/EnvironmentVariables.sh
tools/Gauss2Gro-OPLS.py
tools/GenerateQMData.py
tools/MatchFormatting.py
tools/ParseInputFile.py
tools/ReadForceField.py
tools/SelfConsistentCycle.py
tools/TagMol2.py
tools/dscan.py
tools/explain-gaff.py
tools/explain-opls.py
tools/filecnv.py
tools/gro2arc-amoeba-water.py
tools/install-cctools-41.sh
tools/install-cctools-43.sh
tools/install-cctools-60.sh
tools/ESP/draw-esp.vmd
tools/ESP/esp-hf631gs.esp
tools/ESP/esp-hf631gs.espx
tools/ESP/esp-hf631gs.out
tools/ESP/esp-hf631gs.xyz
tools/ESP/read-esp.py
tools/ESP/qchem-cubes/About.txt
tools/ESP/qchem-cubes/cubediff.py
tools/ESP/qchem-cubes/qcubegen2.py
tools/drawforces/MMforce.xyz
tools/drawforces/QMatoms.gro
tools/drawforces/QMforce.xyz
tools/drawforces/drawforces.vmd
tools/vibrations/anifrq-tc.py
tools/vibrations/anifrq.py
tools/vibrations/freq-opt.qchem.out
tools/vibrations/frequency.gaussian.com
tools/vibrations/frequency.gaussian.out
tools/vibrations/frequency.psi.dat
tools/vibrations/frequency.psi4.out
tools/vibrations/frequency.qchem.in
tools/vibrations/frequency.qchem.out
tools/vibrations/make-vdata.py
tools/vibrations/vdata.txt