├── .github └── workflows │ └── gromacs_installation.yml ├── README.md ├── advanced_lecture_series └── lecture_001.zip ├── large_language_models └── shulgin │ ├── __init__.py │ └── llm.py ├── molecular_dynamics └── simulating_kinases │ ├── step_1 │ ├── README.md │ ├── pdb_files │ │ ├── README │ │ ├── ligand.pdb │ │ ├── model.pdb │ │ └── model.pka │ ├── results │ │ ├── step1_out_model.crd │ │ ├── step1_out_model.pdb │ │ ├── step1_out_model.psf │ │ ├── step1_out_protein.crd │ │ ├── step1_out_protein.pdb │ │ └── step1_out_protein.psf │ ├── run.inp │ └── toppar.str │ ├── step_2 │ ├── .run.inp.swp │ ├── results │ │ ├── step2_h_xwat.crd │ │ ├── step2_h_xwat.pdb │ │ └── step2_h_xwat.psf │ ├── run.inp │ └── water_xray.pdb │ └── toppar │ ├── 00toppar_file_format.txt │ ├── ace │ ├── acepar19.inp │ ├── acepar22_prot.inp │ └── acepar27_na.inp │ ├── cheq │ ├── par_all30_cheq_prot.inp │ └── top_all30_cheq_prot.inp │ ├── drude │ ├── drude_toppar_2019.tgz │ └── positive_drude.tgz │ ├── gbsw │ ├── 00readme │ ├── par_all22_prot_gbsw.inp │ ├── radii_prot_na.str │ └── radius_gbsw.str │ ├── larmord │ └── larmord_rna.dat │ ├── metals │ └── CHARMM_METAL.tgz │ ├── non_charmm │ ├── 00readme │ ├── gromacs │ │ └── charmm36-mar2019.ff.tgz │ ├── par_amber_98.inp │ ├── par_amber_cornell.inp │ ├── par_bms_dec03.inp │ ├── par_opls_aa.inp │ ├── par_opls_aam.inp │ ├── par_opls_ligand.inp │ ├── parm14sb_all.prm │ ├── parm14sb_all.rtf │ ├── top_amber_cornell.inp │ ├── top_bms_dec03.inp │ ├── top_opls_aa.inp │ ├── top_opls_aam.inp │ ├── toppar_chloroform_dh.str │ ├── toppar_ions_nbfix_uiuc.str │ ├── toppar_water_ions_spc.str │ ├── toppar_water_ions_spc_e.str │ ├── toppar_water_ions_tip3p_pme_b.str │ ├── toppar_water_ions_tip3p_pme_f.str │ ├── toppar_water_ions_tip4p.str │ ├── toppar_water_ions_tip4p_2005.str │ ├── toppar_water_ions_tip4p_ew.str │ ├── toppar_water_ions_tip5p.str │ └── toppar_water_ions_tip5p_ew.str │ ├── openmm_gbsaobc2 │ ├── charmm_all36_na_gbsaobc.str │ ├── charmm_all36_prot+na_gbsaobc.str │ ├── charmm_all36_prot_gbsaobc.str │ └── makednarna_obc.pl │ ├── par_all22_prot.prm │ ├── par_all35_ethers.prm │ ├── 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_hbond.inp │ ├── param19.inp │ ├── rush │ ├── par_rush_058.inp │ ├── par_rush_058_a.cmap │ └── top_rush_058.inp │ ├── silicates │ ├── 00README │ ├── code │ │ ├── cell.f │ │ ├── compile.txt │ │ ├── crystal.dat │ │ ├── crystal.f │ │ ├── input.xyz │ │ ├── patches.dat │ │ ├── patchfind.f │ │ └── patchfind.x │ ├── crystal.dat │ ├── crystal.img │ ├── image_patch.str │ ├── input.xyz │ ├── params.str │ ├── patches.dat │ ├── quartz_init.pdb │ ├── supp_mat_oct05.tar │ ├── test.inp │ ├── test.log │ ├── test.out │ ├── test_opt.crd │ ├── test_opt.pdb │ ├── test_opt.psf │ └── toppar │ │ ├── par_silicates.inp │ │ └── top_silicates.inp │ ├── stream │ ├── carb │ │ ├── toppar_all36_carb_glycolipid.str │ │ ├── toppar_all36_carb_glycopeptide.str │ │ ├── toppar_all36_carb_imlab.str │ │ ├── toppar_all36_carb_lignin.str │ │ └── toppar_all36_carb_model.str │ ├── cphmd │ │ └── protpatch_protein_toppar36.str │ ├── lipid │ │ ├── toppar_all36_lipid_bacterial.str │ │ ├── toppar_all36_lipid_cardiolipin.str │ │ ├── toppar_all36_lipid_cationpi_wyf.str │ │ ├── toppar_all36_lipid_cholesterol.str │ │ ├── toppar_all36_lipid_detergent.str │ │ ├── toppar_all36_lipid_ether.str │ │ ├── toppar_all36_lipid_inositol.str │ │ ├── toppar_all36_lipid_list.str │ │ ├── toppar_all36_lipid_lps.str │ │ ├── toppar_all36_lipid_miscellaneous.str │ │ ├── toppar_all36_lipid_model.str │ │ ├── toppar_all36_lipid_prot.str │ │ ├── toppar_all36_lipid_sphingo.str │ │ └── toppar_all36_lipid_yeast.str │ ├── misc │ │ ├── toppar_amines.str │ │ ├── toppar_dum_noble_gases.str │ │ ├── toppar_hbond.str │ │ └── toppar_ions_won.str │ ├── na │ │ ├── toppar_all36_na_model.str │ │ ├── toppar_all36_na_modifications.str │ │ ├── toppar_all36_na_nad_ppi.str │ │ ├── toppar_all36_na_reactive_rna.str │ │ └── toppar_all36_na_rna_modified.str │ └── prot │ │ ├── toppar_all36_prot_aldehydes.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_pyridines.str │ │ └── toppar_all36_prot_retinol.str │ ├── tamdfff │ ├── par_all22_prot_tadcmap.ahbb4.inp │ ├── par_tadmap.chi1.ahbb4.inp │ └── top_all22_prot_cmap.ahbb4.inp │ ├── tip216.crd │ ├── top_all22_prot.rtf │ ├── top_all35_ethers.rtf │ ├── top_all36_carb.rtf │ ├── top_all36_cgenff.rtf │ ├── top_all36_lipid.rtf │ ├── top_all36_na.rtf │ ├── top_all36_prot.rtf │ ├── toph19.inp │ ├── toppar_all.history │ ├── toppar_all.history~ │ └── toppar_water_ions.str └── simulation └── 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