├── CLUSTERING_ANALYSIS ├── README ├── cluster-A.dat.jpg ├── cluster-B.dat.jpg ├── cluster-D.dat.jpg ├── clustering.tcl └── total_clusters.dat.jpg ├── Count_SS.f90 ├── Count_water.tcl ├── Coustamized_VMD_Commands ├── README ├── analysis.tcl └── user_manual_for_analysis_script_V1.pdf ├── Distance_bwn_two_group_of_atoms.tcl ├── Extract_phi_psi.tcl ├── Print_Residues_around_selection.tcl ├── README.md ├── Secondary_structural_analysis_RAMCHANDRAN-PLOT ├── A_HELIX-fluctuation.dat ├── A_HELIX.gnp ├── A_HELIX.jpg ├── B_Sheet-fluctuation.dat ├── B_sheet.gnp ├── B_sheet.jpg ├── PSIPHI.dat ├── README ├── plotting.sh ├── rama_plot.gnp ├── rama_plot.jpg └── ramachandran_plot.tcl ├── angle-details.dat ├── angle.dat ├── angle_V2-details.dat ├── angle_V2.dat ├── angle_btw_three_atoms_V1.tcl ├── angle_btw_three_atoms_V2.tcl ├── avg_str_anji.tcl ├── dist_two_atoms_V1.tcl ├── dist_two_atoms_V2.tcl ├── distance_distribution.tcl ├── end-to-end_dostance.tcl ├── get_interactions.tcl ├── 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