├── .gitignore ├── LICENSE ├── README.md ├── Scripts ├── fold.py ├── folder ├── impicit_sim.py ├── ligconfgen.py ├── ligcvgen.py ├── omm │ ├── __init__.py │ ├── new_omm_readparams.py │ ├── omm_barostat.py │ ├── omm_readinputs.py │ ├── omm_readparams.py │ ├── omm_restraints.py │ ├── omm_rewrap.py │ ├── omm_simulator.py │ ├── omm_vfswitch.py │ └── openmm_run.py ├── openmm_simulator.py ├── openmmsim.py ├── pcagen.py ├── steer ├── unbind ├── unbind.py ├── unfold.py └── unfolder ├── environment.yml └── examples ├── 2JOF ├── charmm22star.ff │ ├── aminoacids.arn │ ├── aminoacids.c.tdb │ ├── aminoacids.hdb │ ├── aminoacids.n.tdb │ ├── aminoacids.r2b │ ├── aminoacids.rtp │ ├── aminoacids.vsd │ ├── atomtypes.atp │ ├── cmap.itp │ ├── dna.arn │ ├── dna.c.tdb │ ├── dna.hdb │ ├── dna.n.tdb │ ├── dna.rtp │ ├── ffbonded.itp │ ├── ffnabonded.itp │ ├── ffnanonbonded.itp │ ├── ffnonbonded.itp │ ├── forcefield.doc │ ├── forcefield.itp │ ├── gb.itp │ ├── ions.itp │ ├── lipids.hdb │ ├── lipids.rtp │ ├── rna.arn │ ├── rna.c.tdb │ ├── rna.hdb │ ├── rna.n.tdb │ ├── rna.r2b │ ├── rna.rtp │ ├── spc.itp │ ├── spce.itp │ ├── tip3p.itp │ ├── tip4p.itp │ ├── tip4pew.itp │ ├── tip5p.itp │ ├── tips3p.itp │ └── watermodels.dat ├── equili.gro ├── folded.gro ├── folded.pdb ├── posre.itp ├── system.py └── topol.top ├── 3PTB ├── ben │ ├── 3ptb_hetb.mol │ ├── 3ptb_hetb.pdb │ ├── 3ptb_hetb_h.mol │ ├── BEN.mol2 │ ├── BEN_csml.yml │ ├── ben.sdf │ ├── csmlMap.py │ ├── csml_results.yml │ ├── draw2graph.py │ ├── drawing.gpickle │ ├── drawing_2D.mol │ ├── drawing_3D.mol │ └── drawing_no_h.gpickle ├── equil.gro ├── pca_model.pkl ├── step3_input.crd ├── step3_input.pdb ├── step3_input.psf ├── step5_production.inp ├── sysinfo.dat ├── system.py ├── toppar.str └── toppar │ ├── cam.str │ ├── par_all36_carb.prm │ ├── par_all36_cgenff.prm │ ├── par_all36_lipid.prm │ ├── par_all36_na.prm │ ├── par_all36_prot.prm │ ├── par_all36m_prot.prm │ ├── par_interface.prm │ ├── tip216.crd │ ├── top_all36_carb.rtf │ ├── top_all36_cgenff.rtf │ ├── top_all36_lipid.rtf │ ├── top_all36_na.rtf │ ├── top_all36_prot.rtf │ ├── top_interface.rtf │ ├── toppar_all36_carb_glycolipid.str │ ├── toppar_all36_carb_glycopeptide.str │ ├── toppar_all36_carb_imlab.str │ ├── toppar_all36_label_fluorophore.str │ ├── toppar_all36_label_spin.str │ ├── toppar_all36_lipid_archaeal.str │ ├── toppar_all36_lipid_bacterial.str │ ├── toppar_all36_lipid_cardiolipin.str │ ├── toppar_all36_lipid_cholesterol.str │ ├── toppar_all36_lipid_dag.str │ ├── toppar_all36_lipid_detergent.str │ ├── toppar_all36_lipid_ether.str │ ├── toppar_all36_lipid_hmmm.str │ ├── toppar_all36_lipid_inositol.str │ ├── toppar_all36_lipid_lnp.str │ ├── toppar_all36_lipid_lps.str │ ├── toppar_all36_lipid_miscellaneous.str │ ├── toppar_all36_lipid_model.str │ ├── toppar_all36_lipid_mycobacterial.str │ ├── toppar_all36_lipid_oxidized.str │ ├── toppar_all36_lipid_prot.str │ ├── toppar_all36_lipid_sphingo.str │ ├── toppar_all36_lipid_tag.str │ ├── toppar_all36_lipid_yeast.str │ ├── toppar_all36_moreions.str │ ├── toppar_all36_na_nad_ppi.str │ ├── toppar_all36_na_rna_modified.str │ ├── toppar_all36_nano_lig.str │ ├── toppar_all36_nano_lig_patch.str │ ├── toppar_all36_polymer_solvent.str │ ├── toppar_all36_prot_arg0.str │ ├── toppar_all36_prot_c36_d_aminoacids.str │ ├── toppar_all36_prot_c36m_d_aminoacids.str │ ├── toppar_all36_prot_fluoro_alkanes.str │ ├── toppar_all36_prot_heme.str │ ├── toppar_all36_prot_model.str │ ├── toppar_all36_prot_modify_res.str │ ├── toppar_all36_prot_na_combined.str │ ├── toppar_all36_prot_retinol.str │ ├── toppar_all36_synthetic_polymer.str │ ├── toppar_all36_synthetic_polymer_patch.str │ ├── toppar_dum_noble_gases.str │ ├── toppar_ions_won.str │ └── toppar_water_ions.str ├── 4W52 ├── 4w52_pca.pkl ├── bnz.itp ├── md.mdp ├── pbcmol.gro ├── pca_model.pkl ├── posre.itp ├── posre_BNZ.itp ├── system.py └── topol.top └── NTL9 ├── ntl9.prmtop ├── reference.pdb ├── system.py └── unfolded.pdb /.gitignore: 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