├── .gitignore ├── AMBER ├── 4cpptraj.sh └── mmgbsa.sh ├── GROMACS ├── 16_GPCR_MARTINI_MD │ ├── Protein.itp │ ├── analyse_oligomers.sh │ ├── chain_ .ssd │ ├── index.ndx │ ├── martini_ff │ │ ├── martini_chol_hinge_p30.itp │ │ ├── martini_v2.0_ions.itp │ │ ├── martini_v2.0_lipids.itp │ │ ├── martini_v2.0_lipids_all_201506.itp │ │ ├── martini_v2.0_solvents.itp │ │ ├── martini_v2.2.itp │ │ ├── martini_v2.2P.itp │ │ ├── martini_v2.2P_aminoacids.itp │ │ ├── martini_v2.2_aminoacids.itp │ │ └── martini_v2.P.itp │ ├── mdp │ │ ├── dynamic.mdp │ │ ├── equil.mdp │ │ ├── equil_long.mdp │ │ ├── equil_long2.mdp │ │ ├── equil_long3.mdp │ │ └── minim.mdp │ ├── readme.txt │ ├── run.sh │ ├── run_gpu.sh │ ├── system_start.cpt │ ├── system_start.gro │ └── topol.top ├── GPCR │ ├── README │ ├── index.ndx │ ├── psf2itp.py │ ├── restraints │ │ ├── POPC_rest.itp │ │ └── PROA_rest.itp │ ├── step5_charmm2gmx.crd │ ├── step5_charmm2gmx.oldpsf │ ├── step5_charmm2gmx.pdb │ ├── step5_charmm2gmx.psf │ ├── step5_charmm2gmx_memb.str │ ├── step5_charmm2gmx_prot.str │ ├── step5_charmm2gmx_rest.py │ ├── step6.0_minimization.mdp │ ├── step6.1_equilibration.mdp │ ├── step6.2_equilibration.mdp │ ├── step6.3_equilibration.mdp │ ├── step6.4_equilibration.mdp │ ├── step6.5_equilibration.mdp │ ├── step6.6_equilibration.mdp │ ├── step7_production.mdp │ ├── topol.top │ └── toppar │ │ ├── CLA.itp │ │ ├── POPC.itp │ │ ├── POT.itp │ │ ├── PROA.itp │ │ ├── TIP3.itp │ │ └── charmm36.itp ├── Trajectory_analysis_scripts │ ├── PCA_GMX.sh │ ├── extract_info.sh │ └── structure_analysis_GMX.sh ├── beginner │ ├── .gitignore │ ├── 1Q3L.pdb │ ├── README.md │ ├── equil.mdp │ ├── ions.mdp │ ├── mdout.mdp │ ├── minim.mdp │ ├── prod.mdp │ ├── tutorial.ipynb │ └── xvg_plot.py ├── biomembrane │ ├── burn_bilayer.sh │ ├── readme.txt │ └── ref │ │ └── popc_bilayer │ │ ├── System.cpt │ │ ├── System.gro │ │ ├── System.ndx │ │ ├── System.top │ │ ├── restraints │ │ └── POPC_rest.itp │ │ └── toppar │ │ ├── CLA.itp │ │ ├── POPC.itp │ │ ├── POT.itp │ │ ├── TIP3.itp │ │ └── charmm36.itp └── nucl │ ├── Installation_notes.md │ ├── README.md │ └── docs │ ├── 1kx5.pdb │ ├── 1kx5.pka │ ├── 1kx5.propka_input │ ├── EM.png │ ├── PF_1kx5.fxout │ ├── README.md │ ├── Unrecognized_molecules.txt │ ├── beta.png │ ├── cutting.jpg │ ├── cutting2.png │ ├── cutting3.png │ ├── histidine.png │ ├── ions.mdp │ ├── ions.png │ ├── md.mdp │ ├── minim.mdp │ ├── npt.mdp │ ├── nvt.mdp │ ├── propka_code.ipynb │ ├── ready_sys.png │ ├── understanding1.png │ ├── understanding2.png │ ├── understanding3.png │ ├── understanding4.png │ └── water.png ├── MD ├── .DS_Store └── NAMD │ ├── .DS_Store │ └── nucl │ ├── nucleosome_AMBER │ ├── prep │ │ ├── align_nucl.tcl │ │ ├── gen_cons.tcl │ │ ├── gen_nucl.leap │ │ ├── par_all27_prot_na.prm │ │ ├── par_all36_na.prm │ │ ├── par_all36_prot.prm │ │ ├── par_water_ions_36.prm │ │ ├── psfgen_1kx5_notails_ge_cons.tcl │ │ ├── top_all27_prot_na.rtf │ │ ├── top_all36_na.rtf │ │ ├── top_all36_prot.rtf │ │ └── top_water_ions_36.rtf │ └── simul │ │ ├── analysis_scripts_amb │ │ ├── .Rapp.history │ │ ├── .Rhistory │ │ ├── 0prepare.sh │ │ ├── 1fast_visual.sh │ │ ├── 2gen_move.sh │ │ ├── 3ions.sh │ │ ├── 4water.sh │ │ ├── 5dna.sh │ │ ├── 5dna_2.sh │ │ ├── 6contacts.sh │ │ ├── 7energy.sh │ │ ├── 8epotential.sh │ │ ├── 99pub_graphs.sh │ │ ├── Rplots.pdf │ │ ├── arg_hist.vmdpy │ │ ├── arg_pos.vmdpy │ │ ├── arg_rmsf.tcl │ │ ├── at_fluct.vmdpy │ │ ├── atomic_fluct.py │ │ ├── av_struct 2.tcl │ │ ├── av_struct.tcl │ │ ├── b_fact.tcl │ │ ├── check_image_int.tcl │ │ ├── cluster_md.tcl │ │ ├── create_aligned_pdb.tcl │ │ ├── create_aligned_pdb2.vmdpy │ │ ├── def_struct_param.tcl │ │ ├── dif_av_cryst.tcl │ │ ├── dist.tcl │ │ ├── dna2_analyze_dyn.r │ │ ├── dna2_avr_analyze_dna_param.r │ │ ├── dna2_avr_analyze_geom.r │ │ ├── dna2_df_to_avr.r │ │ ├── dna2_df_to_corr.r │ │ ├── dna2_get_df_cryst.vmdpy │ │ ├── dna2_get_df_md.vmdpy │ │ ├── dna_bb_analyze.r │ │ ├── dna_bl_analyze.r │ │ ├── dna_bl_geom.tcl │ │ ├── dna_bl_recombine.py │ │ ├── dna_gr_analyze.r │ │ ├── dna_hbonds_md.r │ │ ├── dna_hbonds_md.sh │ │ ├── dna_hbonds_md.tcl │ │ ├── dna_par_3dna_analyze.r │ │ ├── dna_par_3dna_analyze_av.r │ │ ├── dna_par_3dna_analyze_heatmaps.r │ │ ├── dna_par_3dna_analyze_hist.r │ │ ├── dna_par_3dna_recombine.py │ │ ├── dna_par_analyze.py │ │ ├── dna_par_cur_recombine.py │ │ ├── dna_par_labels │ │ │ ├── .Rapp.history │ │ │ ├── Buckle.png │ │ │ ├── Opening.png │ │ │ ├── Prop.Tw.png │ │ │ ├── Rise.png │ │ │ ├── Roll.png │ │ │ ├── Shear.png │ │ │ ├── Shift.png │ │ │ ├── Slide.png │ │ │ ├── Stagger.png │ │ │ ├── Stretch.png │ │ │ ├── Tilt.png │ │ │ └── Twist.png │ │ ├── dna_param.py │ │ ├── dna_param.pyc │ │ ├── dna_params_3dna.tcl │ │ ├── dna_params_cur.tcl │ │ ├── dna_prot_contact_map.sh │ │ ├── dna_prot_contact_map.tcl │ │ ├── dna_prot_contacts_md.r │ │ ├── dna_prot_contacts_md.sh │ │ ├── dna_prot_contacts_md.tcl │ │ ├── dna_prot_contacts_visual.tcl │ │ ├── dna_prot_hbonds_md.r │ │ ├── dna_prot_hbonds_md.sh │ │ ├── dna_prot_hbonds_md.tcl │ │ ├── dna_rmsd.r │ │ ├── dna_rmsd.tcl │ │ ├── dna_rot_all_to_avr.r │ │ ├── dna_rot_get_df.vmdpy │ │ ├── dna_wat_prot_hbonds_md.r │ │ ├── dna_wat_prot_hbonds_md.sh │ │ ├── dna_wat_prot_hbonds_md.tcl │ │ ├── dnabb_covar.py │ │ ├── dnabb_covar.pyc │ │ ├── dnabb_cross_corr.py │ │ ├── dnabb_cross_corr.pyc │ │ ├── dnabb_var_covar.pyc │ │ ├── eda_show.tcl │ │ ├── energies_md.sh │ │ ├── energies_min_eq.sh │ │ ├── extr_nucl_dcd_md.tcl │ │ ├── extr_nucl_dcd_min_eq.tcl │ │ ├── extr_nucl_solv_dcd_md.tcl │ │ ├── fake_volrend.sh │ │ ├── fake_volrend_2ions.sh │ │ ├── fake_volrend_colorbar.sh │ │ ├── fast_render │ │ │ ├── add_text_layer.tcl │ │ │ ├── input_param.tcl │ │ │ ├── make_movie.sh │ │ │ └── movie.tcl │ │ ├── get_rmsf.sh │ │ ├── h3-4h-bundle_dist.tcl │ │ ├── hfolds_covar.py │ │ ├── hfolds_covar.pyc │ │ ├── hfolds_cross_corr.py │ │ ├── hfolds_cross_corr.pyc │ │ ├── hfolds_dist.tcl │ │ ├── hfolds_var_covar.pyc │ │ ├── int_analyze.sh │ │ ├── int_dna_prot.r │ │ ├── int_dna_prot_Z.r │ │ ├── int_dna_prot_Z_s2.r │ │ ├── int_dna_prot_sym_prof.r │ │ ├── int_dna_prot_var.r │ │ ├── int_get_ions_raw.vmdpy │ │ ├── int_get_nucl_prot_raw.vmdpy │ │ ├── int_get_prot_prot_raw.vmdpy │ │ ├── int_get_raw.sh │ │ ├── int_get_raw_nucl_prot_AMB.vmdpy │ │ ├── int_get_wat_dna_raw_old.vmdpy │ │ ├── int_get_wat_raw.vmdpy │ │ ├── int_ions.r │ │ ├── int_ions_sym_prof.r │ │ ├── int_prot_prot.r │ │ ├── int_raw_to_avr_dna_prot_AMB_old.r │ │ ├── int_raw_to_avr_dna_prot_AMB_provis.r │ │ ├── int_raw_to_avr_ions.r │ │ ├── int_raw_to_avr_prot_prot.r │ │ ├── int_raw_to_avr_wat.r │ │ ├── int_raw_to_avr_wat_dna.r │ │ ├── int_resid_resname.vmdpy │ │ ├── int_total_stat.r │ │ ├── int_wat.r │ │ ├── int_wat_details │ │ │ ├── .Rapp.history │ │ │ ├── Rplots.pdf │ │ │ ├── int_get_wat_raw.vmdpy │ │ │ ├── int_get_wat_raw_cryst.vmdpy │ │ │ ├── int_raw_to_avr_wat.r │ │ │ └── int_wat.r │ │ ├── int_wat_dna.r │ │ ├── int_wat_sym_prof.r │ │ ├── ion_atm.tcl │ │ ├── ion_rdf.tcl │ │ ├── ion_volmap.tcl │ │ ├── libs │ │ │ └── bfactor.tcl │ │ ├── max_rmsf_ca.tcl │ │ ├── myPrody.py │ │ ├── myPrody.pyc │ │ ├── myplot.py │ │ ├── myplot_cluster.py │ │ ├── myplot_dna_par.py │ │ ├── myplot_dna_prot_map.py │ │ ├── myplot_dna_prot_prof.py │ │ ├── myplot_ener.py │ │ ├── myplot_prot_dna_prof.py │ │ ├── myplot_rmsf.py │ │ ├── myplot_rmsf_exp.py │ │ ├── myplot_rmsf_exp_dna.py │ │ ├── myplot_rmsf_exp_sch.py │ │ ├── namdplot.py │ │ ├── overlayed_img │ │ │ ├── add_text_layer.tcl │ │ │ ├── make_overlayed_img.sh │ │ │ ├── over_back.tcl │ │ │ ├── over_bottom.tcl │ │ │ ├── over_front.tcl │ │ │ ├── over_left.tcl │ │ │ └── over_right.tcl │ │ ├── parts_rmsd.r │ │ ├── parts_rmsd.sh │ │ ├── parts_rmsd.tcl │ │ ├── pca.py │ │ ├── pca.sh │ │ ├── pca_dna.py │ │ ├── pca_hfolds.py │ │ ├── prody_analysis.py │ │ ├── pub_dna2_fluct.r │ │ ├── pub_dna2_path.r │ │ ├── pub_dna2_path_ensemble.r │ │ ├── pub_dna_prot_base_prof.r │ │ ├── pub_dna_prot_sugar_prof.r │ │ ├── pub_dna_rmsd.r │ │ ├── pub_dna_rmsd.tcl │ │ ├── pub_dna_rmsf.r │ │ ├── pub_dna_rmsf_rot_sym.r │ │ ├── pub_dna_rot.r │ │ ├── pub_int_dna_prot2.r │ │ ├── pub_int_dna_prot_main_stable_sites.r │ │ ├── pub_int_dna_prot_main_stable_sites_expanded.r │ │ ├── pub_prot_rmsd.r │ │ ├── pub_prot_rmsd.tcl │ │ ├── pub_prot_rmsd_bars.r │ │ ├── pub_prot_rmsd_bars2.r │ │ ├── pub_prot_rmsd_sch.r │ │ ├── pub_prot_rmsd_sch.tcl │ │ ├── pub_prot_rmsf.r │ │ ├── pub_rmsd_md.sh │ │ ├── pub_rmsd_md_cryst.tcl │ │ ├── readme.txt │ │ ├── render_scripts │ │ │ ├── add_text_layer.tcl │ │ │ ├── gen_render.sh │ │ │ ├── gen_run_vmd.sh │ │ │ ├── help_scr │ │ │ │ ├── addb.sh │ │ │ │ └── addf.sh │ │ │ ├── input_param.tcl │ │ │ ├── movie.tcl │ │ │ ├── movie_msms.tcl │ │ │ ├── movie_msms_sm.tcl │ │ │ ├── movie_msms_sm_grad.tcl │ │ │ ├── over_img.tcl │ │ │ ├── run_vmd.sh │ │ │ └── run_vmd_batched.sh │ │ ├── rmsd_md.sh │ │ ├── rmsd_md_av.tcl │ │ ├── rmsd_md_cryst.tcl │ │ ├── rmsd_min_eq.sh │ │ ├── rmsd_min_eq.tcl │ │ ├── rmsf.tcl │ │ ├── rmsf_cryst.tcl │ │ ├── run_curves.sh │ │ ├── run_x3dna.sh │ │ ├── run_x3dna_bl.sh │ │ ├── symmetry_rmsd.sh │ │ ├── symmetry_rmsd.tcl │ │ ├── sync_local.sh │ │ ├── transformations.py │ │ ├── transformations.pyc │ │ ├── twist.r │ │ ├── vhq.tcl │ │ ├── view.sh │ │ ├── view_1kx5.tcl │ │ ├── view_b_factors.sh │ │ ├── view_nucl_aver.tcl │ │ ├── view_nucl_md_hq.tcl │ │ ├── view_nucl_md_sol.sh │ │ ├── view_nucl_min_eq.sh │ │ ├── view_rmsf.sh │ │ ├── visual_arg_comp.tcl │ │ ├── visual_dif_av_cryst.tcl │ │ ├── visual_dif_av_cryst_overl.tcl │ │ ├── visual_eda_dna.tcl │ │ ├── visual_eda_dna_old.tcl │ │ ├── visual_eda_hfolds.tcl │ │ ├── visual_eda_hfolds_old.tcl │ │ ├── visual_rmsf.tcl │ │ ├── visual_rmsf_cryst.tcl │ │ ├── visual_rmsf_sch.tcl │ │ ├── water_distr.tcl │ │ ├── water_volmap.tcl │ │ └── water_volmap_msms.tcl │ │ ├── input │ │ ├── md.conf │ │ ├── min_equil.conf │ │ ├── par_all36_na.prm │ │ ├── par_all36_prot.prm │ │ └── par_water_ions_36.prm │ │ ├── lomo_cp_back.sh │ │ ├── lomo_run_md.sh │ │ ├── lomo_run_min_eq.sh │ │ ├── pull.sh │ │ ├── push.sh │ │ └── run_min_eq_md.sh │ └── nucleosome_CHARMM │ ├── prep │ ├── par_all27_prot_na.prm │ ├── par_all36_na.prm │ ├── par_all36_prot.prm │ ├── par_water_ions_36.prm │ ├── psfgen_nucl_link_cons_zw.tcl │ ├── top_all27_prot_na.rtf │ ├── top_all36_na.rtf │ ├── top_all36_prot.rtf │ ├── top_water_ions_36.rtf │ └── toppar_water_ions.str │ └── simul │ ├── analysis_scripts_link_zw │ ├── .Rapp.history │ ├── 00_TODO.txt │ ├── 0prepare.sh │ ├── 1fast_visual.sh │ ├── 2gen_move.sh │ ├── 3ions.sh │ ├── 4water.sh │ ├── 5dna.sh │ ├── 5dna_2.sh │ ├── 6contacts.sh │ ├── 7energy.sh │ ├── 8epotential.sh │ ├── 99pub_graphs.sh │ ├── Rplots.pdf │ ├── arg_rmsf.tcl │ ├── at_fluct.vmdpy │ ├── atomic_fluct.py │ ├── av_struct.tcl │ ├── b_fact.tcl │ ├── beta20.pdb │ ├── chain_rmsd.r │ ├── chain_rmsd.sh │ ├── chain_rmsd.tcl │ ├── check_image_int.tcl │ ├── cluster_md.tcl │ ├── create_aligned_pdb.tcl │ ├── create_aligned_pdb2.vmdpy │ ├── def_struct_param.tcl │ ├── dif_av_cryst.tcl │ ├── dist.tcl │ ├── dna2_analyze_dyn.r │ ├── dna2_avr_analyze_dna_param.r │ ├── dna2_avr_analyze_dna_param_poster.r │ ├── dna2_avr_analyze_geom.r │ ├── dna2_df_to_avr.r │ ├── dna2_df_to_corr.r │ ├── dna2_get_df_cryst.vmdpy │ ├── dna2_get_df_md.vmdpy │ ├── dna_bb_analyze.r │ ├── dna_bl_analyze.r │ ├── dna_bl_geom.tcl │ ├── dna_bl_recombine.py │ ├── dna_gr_analyze.r │ ├── dna_hbonds_md.r │ ├── dna_hbonds_md.sh │ ├── dna_hbonds_md.tcl │ ├── dna_par_3dna_analyze.r │ ├── dna_par_3dna_analyze_av.r │ ├── dna_par_3dna_analyze_heatmaps.r │ ├── dna_par_3dna_analyze_hist.r │ ├── dna_par_3dna_recombine.py │ ├── dna_par_analyze.py │ ├── dna_par_cur_recombine.py │ ├── dna_par_labels │ │ ├── .Rapp.history │ │ ├── Buckle.png │ │ ├── Opening.png │ │ ├── Prop.Tw.png │ │ ├── Rise.png │ │ ├── Roll.png │ │ ├── Shear.png │ │ ├── Shift.png │ │ ├── Slide.png │ │ ├── Stagger.png │ │ ├── Stretch.png │ │ ├── Tilt.png │ │ └── Twist.png │ ├── dna_param.py │ ├── dna_param.pyc │ ├── dna_params_3dna.tcl │ ├── dna_params_cur.tcl │ ├── dna_prot_contact_map.sh │ ├── dna_prot_contact_map.tcl │ ├── dna_prot_contacts_md.r │ ├── dna_prot_contacts_md.sh │ ├── dna_prot_contacts_md.tcl │ ├── dna_prot_contacts_visual.tcl │ ├── dna_prot_hbonds_md.r │ ├── dna_prot_hbonds_md.sh │ ├── dna_prot_hbonds_md.tcl │ ├── dna_rmsd.r │ ├── dna_rmsd.tcl │ ├── dna_rot_all_to_avr.r │ ├── dna_rot_get_df.vmdpy │ ├── dna_wat_prot_hbonds_md.r │ ├── dna_wat_prot_hbonds_md.sh │ ├── dna_wat_prot_hbonds_md.tcl │ ├── dnabb_covar.py │ ├── dnabb_covar.pyc │ ├── dnabb_cross_corr.py │ ├── dnabb_cross_corr.pyc │ ├── dnabb_var_covar.pyc │ ├── eda_show.tcl │ ├── energies_md.sh │ ├── energies_min_eq.sh │ ├── extr_nucl_dcd_md.tcl │ ├── extr_nucl_dcd_min_eq.tcl │ ├── extr_nucl_solv_dcd_md.tcl │ ├── fake_volrend.sh │ ├── fake_volrend_2ions.sh │ ├── fake_volrend_colorbar.sh │ ├── fast_render │ │ ├── add_text_layer.tcl │ │ ├── input_param.tcl │ │ ├── make_movie.sh │ │ ├── movie.tcl │ │ └── movie_dyad.tcl │ ├── get_rmsf.sh │ ├── grisha_sasa_footprint.tcl │ ├── h3-4h-bundle_dist.tcl │ ├── hfolds_covar.py │ ├── hfolds_covar.pyc │ ├── hfolds_cross_corr.py │ ├── hfolds_cross_corr.pyc │ ├── hfolds_dist.tcl │ ├── hfolds_var_covar.pyc │ ├── ind_dna_prot_wm_poster.r │ ├── int_analyze.sh │ ├── int_get_raw.sh │ ├── int_get_raw_ions.vmdpy │ ├── int_get_raw_ions_cryst.vmdpy │ ├── int_get_raw_nucl_prot.vmdpy │ ├── int_get_raw_nucl_prot_cryst.vmdpy │ ├── int_get_raw_prot_prot.vmdpy │ ├── int_get_raw_prot_prot_cryst.vmdpy │ ├── int_get_raw_wat.vmdpy │ ├── int_get_raw_wat_cryst.vmdpy │ ├── int_get_raw_wat_dna.vmdpy │ ├── int_get_raw_wat_dna_cryst.vmdpy │ ├── int_plot.sh │ ├── int_plot_dna_prot.r │ ├── int_plot_dna_prot_Z.r │ ├── int_plot_dna_prot_Z_s2.r │ ├── int_plot_dna_prot_akak.r │ ├── int_plot_dna_prot_anya_talk.r │ ├── int_plot_dna_prot_core_maps.r │ ├── int_plot_dna_prot_core_maps_cryst.r │ ├── int_plot_dna_prot_full_maps.r │ ├── int_plot_dna_prot_full_maps_cryst.r │ ├── int_plot_dna_prot_stat_Z.r │ ├── int_plot_dna_prot_sym_prof.r │ ├── int_plot_dna_prot_var.r │ ├── int_plot_ions.r │ ├── int_plot_ions_sym_prof.r │ ├── int_plot_prot_prot.r │ ├── int_plot_prot_prot_H2AZ.r │ ├── int_plot_prot_prot_H2AZ_maps_MD.r │ ├── int_plot_prot_prot_H2AZ_maps_cryst.r │ ├── int_plot_prot_prot_anya_talk.r │ ├── int_plot_wat.r │ ├── int_plot_wat_dna.r │ ├── int_plot_wat_dna_anya_talk.r │ ├── int_plot_wat_sym_prof.r │ ├── int_raw_to_avr.sh │ ├── int_raw_to_avr_dna_prot.r │ ├── int_raw_to_avr_ions.r │ ├── int_raw_to_avr_prot_prot.r │ ├── int_raw_to_avr_wat.r │ ├── int_raw_to_avr_wat_dna.r │ ├── int_raw_to_max_dna_prot.r │ ├── int_resid_resname.vmdpy │ ├── int_total_stat.r │ ├── int_wat_details │ │ ├── .Rapp.history │ │ ├── Rplots.pdf │ │ ├── int_get_wat_raw.vmdpy │ │ ├── int_get_wat_raw_cryst.vmdpy │ │ ├── int_raw_to_avr_wat.r │ │ └── int_wat.r │ ├── ion_atm.tcl │ ├── ion_atm_dna_all.tcl │ ├── ion_atm_dna_core.tcl │ ├── ion_atm_dna_linker1.tcl │ ├── ion_atm_dna_linker2.tcl │ ├── ion_atm_sphere.tcl │ ├── ion_cons.tcl │ ├── ion_rdf.tcl │ ├── ion_volmap.tcl │ ├── ions_cons.vmdpy │ ├── libs │ │ └── bfactor.tcl │ ├── max_rmsf_ca.tcl │ ├── myPrody.py │ ├── myPrody.pyc │ ├── myplot.py │ ├── myplot_cluster.py │ ├── myplot_dna_par.py │ ├── myplot_dna_prot_map.py │ ├── myplot_dna_prot_prof.py │ ├── myplot_ener.py │ ├── myplot_ions.py │ ├── myplot_prot_dna_prof.py │ ├── myplot_rmsf.py │ ├── myplot_rmsf_exp.py │ ├── myplot_rmsf_exp_dna.py │ ├── myplot_rmsf_exp_sch.py │ ├── namdplot.py │ ├── overlayed_img │ │ ├── add_text_layer.tcl │ │ ├── make_overlayed_img.sh │ │ ├── over_back.tcl │ │ ├── over_back_no_lab.tcl │ │ ├── over_bottom.tcl │ │ ├── over_bottom_no_lab.tcl │ │ ├── over_front.tcl │ │ ├── over_front_no_lab.tcl │ │ ├── over_left.tcl │ │ └── over_right.tcl │ ├── parts_rmsd.r │ ├── parts_rmsd.sh │ ├── parts_rmsd.tcl │ ├── pca.py │ ├── pca.sh │ ├── pca_dna.py │ ├── pca_hfolds.py │ ├── prody_analysis.py │ ├── pub_dna2_fluct.r │ ├── pub_dna2_fret_5bp.r │ ├── pub_dna2_linker_distance.r │ ├── pub_dna2_path.r │ ├── pub_dna2_path_ensemble.r │ ├── pub_dna2_path_ensemble_linkers.r │ ├── pub_dna2_path_ensemble_linkers2.r │ ├── pub_dna_grooves.r │ ├── pub_dna_prot_base_prof.r │ ├── pub_dna_prot_stat.r │ ├── pub_dna_prot_sugar_prof.r │ ├── pub_dna_rmsd.r │ ├── pub_dna_rmsd.tcl │ ├── pub_dna_rmsf.r │ ├── pub_dna_rmsf_rot_sym.r │ ├── pub_dna_rot.r │ ├── pub_int_dna_anch_dyn.r │ ├── pub_int_dna_h4_corsl.r │ ├── pub_int_dna_prot.r │ ├── pub_int_dna_prot2.r │ ├── pub_int_dna_prot2_av_core.r │ ├── pub_int_dna_prot2_cryst.r │ ├── pub_int_dna_prot2_cryst_av_core.r │ ├── pub_int_dna_prot2_grooves.r │ ├── pub_int_dna_prot2_simp.r │ ├── pub_int_dna_prot2_stab.r │ ├── pub_int_dna_prot2_stable_protprof.r │ ├── pub_int_dna_prot_main_stable_sites.r │ ├── pub_int_dna_prot_main_stable_sites_expanded.r │ ├── pub_int_dna_prot_main_stable_sites_tails.r │ ├── pub_int_dna_prot_map_super_stable_all.r │ ├── pub_int_dna_prot_minor_groove_protprof.r │ ├── pub_int_tail_dna_time.r │ ├── pub_ion_equil.tcl │ ├── pub_prot_rmsd.r │ ├── pub_prot_rmsd.tcl │ ├── pub_prot_rmsd_bars.r │ ├── pub_prot_rmsd_bars2.r │ ├── pub_prot_rmsd_sch.r │ ├── pub_prot_rmsd_sch.tcl │ ├── pub_prot_rmsf.r │ ├── pub_prot_rmsf_full.r │ ├── pub_prot_sasa.r │ ├── pub_prot_sasa2.r │ ├── pub_prot_ss.r │ ├── pub_rmsd_md.sh │ ├── pub_rmsd_md_cryst.tcl │ ├── pub_tails_rmsf.r │ ├── readme.txt │ ├── render_scripts │ │ ├── add_text_layer.tcl │ │ ├── gen_render.sh │ │ ├── gen_run_vmd.sh │ │ ├── help_scr │ │ │ ├── addb.sh │ │ │ └── addf.sh │ │ ├── input_param.tcl │ │ ├── movie.tcl │ │ ├── movie_msms.tcl │ │ ├── movie_msms_sm.tcl │ │ ├── movie_msms_sm_grad.tcl │ │ ├── over_img.tcl │ │ ├── run_vmd.sh │ │ └── run_vmd_batched.sh │ ├── rmsd_md.sh │ ├── rmsd_md.tcl │ ├── rmsd_md_core.tcl │ ├── rmsd_min_eq.sh │ ├── rmsd_min_eq.tcl │ ├── rmsf.tcl │ ├── rmsf_cryst.tcl │ ├── run_curves.sh │ ├── run_x3dna.sh │ ├── sasa_average.r │ ├── sasa_footprint.tcl │ ├── sasa_get.vmdpy │ ├── sasa_get_ref.vmdpy │ ├── saxs.py │ ├── saxs.pyc │ ├── saxs_calculations.vmdpy │ ├── saxs_df_to_avr.r │ ├── saxs_plot.r │ ├── seq_img │ │ ├── H2A_full_inv.png │ │ ├── H2Acore_new.png │ │ ├── H2Afull_new_cl.png │ │ ├── H2Afullr.pdf │ │ ├── H2Afullr.png │ │ ├── H2B_full_inv.png │ │ ├── H2Bcore_new.png │ │ ├── H2Bfull_new_cl.png │ │ ├── H3_full_inv.png │ │ ├── H3core_new.png │ │ ├── H3full_new_cl.png │ │ ├── H4_full_inv.png │ │ ├── H4core_new.png │ │ └── H4full_new_cl.png │ ├── special │ │ ├── .Rapp.history │ │ ├── anya_h2b.r │ │ └── contacts_and_deltaZ.csv │ ├── ss_average.r │ ├── ss_get.vmdpy │ ├── symmetry_rmsd.sh │ ├── symmetry_rmsd.tcl │ ├── sync_local.sh │ ├── tail_linker.vmd │ ├── tails_visual.vmd │ ├── transformations.py │ ├── transformations.pyc │ ├── vhq.tcl │ ├── view.sh │ ├── view_b_factors.sh │ ├── view_nucl_md.sh │ ├── view_nucl_md_hq.tcl │ ├── view_nucl_md_hq_sol.tcl │ ├── view_nucl_md_sol.sh │ ├── view_nucl_min_eq.sh │ ├── view_rmsf.sh │ ├── visual_dif_av_cryst.tcl │ ├── visual_dif_av_cryst_overl.tcl │ ├── visual_eda_dna.tcl │ ├── visual_eda_hfolds.tcl │ ├── visual_rmsf.tcl │ ├── water_distr.tcl │ ├── water_volmap.tcl │ ├── water_volmap_msms.tcl │ └── with_ions.vmd │ ├── input │ ├── md.conf │ ├── md2.conf │ ├── min_equil.conf │ ├── par_all36_na.prm │ ├── par_all36_prot.prm │ └── par_water_ions_36.prm │ ├── lomo_cp_back.sh │ ├── lomo_run_md.sh │ ├── lomo_run_min_eq.sh │ ├── pull.sh │ ├── push.sh │ ├── run_min_eq_md.sh │ └── run_min_eq_md2.sh ├── MDanalysis ├── .ipynb_checkpoints │ └── Nucleosome_dimer_MD_preparation-checkpoint.ipynb ├── 1kx5.pdb ├── GMX_run │ ├── minimization.edr │ ├── minimization.gro │ ├── minimization.log │ ├── minimization.tpr │ └── minimization.trr ├── GMX_system │ ├── charmm36-jul2017.ff │ ├── init.pdb │ ├── init_box.pdb │ ├── posre_Protein_chain_C.itp │ ├── posre_Protein_chain_D.itp │ ├── topol.top │ ├── topol_Protein_chain_C.itp │ └── topol_Protein_chain_D.itp ├── Nucleosome_dimer_MD_preparation.ipynb ├── Protocols │ ├── .ipynb_checkpoints │ │ ├── equilibration-checkpoint.mdp │ │ ├── equilibration_vac-checkpoint.mdp │ │ ├── minimization-checkpoint.mdp │ │ └── production_vac-checkpoint.mdp │ ├── equilibration.mdp │ ├── equilibration_vac.mdp │ ├── minimization.mdp │ ├── production.mdp │ └── production_vac.mdp ├── charmm36-jul2017.ff │ ├── .ipynb_checkpoints │ │ ├── ffbonded-checkpoint.itp │ │ ├── forcefield-checkpoint.doc │ │ ├── forcefield-checkpoint.itp │ │ ├── merged-checkpoint.arn │ │ ├── merged-checkpoint.rtp │ │ ├── merged-checkpoint.vsd │ │ ├── slys-checkpoint.arn │ │ ├── slys-checkpoint.itp │ │ └── slys-checkpoint.rtp │ ├── CGenFF.str │ ├── atomtypes.atp │ ├── cmap.itp │ ├── ffbonded.itp │ ├── ffnonbonded.itp │ ├── forcefield.doc │ ├── forcefield.itp │ ├── gb.itp │ ├── ions.itp │ ├── merged.arn │ ├── merged.c.tdb │ ├── merged.hdb │ ├── merged.n.tdb │ ├── merged.r2b │ ├── merged.rtp │ ├── merged.vsd │ ├── nbfix.itp │ ├── old_c36_cmap.itp │ ├── slys.arn │ ├── slys.itp │ ├── slys.rtp │ ├── spc.itp │ ├── spce.itp │ ├── tip3p.itp │ ├── tip4p.itp │ └── watermodels.dat ├── h2a_h2b_tr.pdb └── mdout.mdp ├── MODELLER ├── .ipynb_checkpoints │ └── examples-checkpoint.ipynb ├── 1HST.pdb ├── 1HST_fit.pdb ├── examples.ipynb ├── humanH1-1HST_A.ali ├── humanH1-1HST_A.pap ├── humanH1.B99990001.pdb ├── humanH1.B99990001_fit.pdb ├── humanH1.D00000001 ├── humanH1.V99990001 ├── humanH1.ali ├── humanH1.ini ├── humanH1.rsr ├── humanH1.sch ├── humanH1_ini.pdb ├── nuc-1AOI.ali ├── nuc-1AOI_mod.ali ├── nuc.B99990001.pdb ├── nuc.B99990002.pdb ├── nuc.B99990003.pdb ├── nuc.B99990004.pdb ├── nuc.B99990005.pdb ├── nuc.BL00010001.pdb ├── nuc.D00000001 ├── nuc.D00000002 ├── nuc.D00000003 ├── nuc.D00000004 ├── nuc.D00000005 ├── nuc.DL00010001 ├── nuc.IL00000001.pdb ├── nuc.V99990001 ├── nuc.V99990002 ├── nuc.V99990003 ├── nuc.V99990004 ├── nuc.V99990005 ├── nuc.ali ├── nuc.ini ├── nuc.lrsr ├── nuc.rsr ├── nuc.sch ├── nucl.ali ├── temp.fasta └── test.ali ├── PLUMED ├── .gitignore ├── README.md ├── funcs.py ├── plumed_WT_metad.ipynb ├── plumed_bias.ipynb ├── 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