repo/
├── analysis
│   ├── interaction_map.html	
│   ├── interaction_map.ipynb			# Jupyter notebook to plot complex interaction map
│   ├── mmgbsa.in
│   ├── mmgbsa.sh						# bash script to run MMGBSA calculation
│   ├── mmgbsa_decomposition_nme1.dat
│   ├── mmgbsa_nme1.out
│   ├── nme1_com_dry.prmtop
│   ├── nme1_lig_dry.prmtop
│   ├── nme1_rec_dry.prmtop
│   ├── plot
│   │   ├── interaction.in
│   │   └── node_nme1_ab.ps
│   └── rmsd_xmgrace.bfile
└── simulation
    ├── a_equilibrium.sh				# bash script to run system equilibration
    ├── b_production.sh					# bash script to run molecular dynamics
    ├── c_lowest_energy_structure.sh	# bash script for output lowest energy PDB structure
    ├── c_mmgbsa_topology.sh			# bash script to generate prmtop files for MMGBSA calculation
    ├── c_nme1_prod_200.crd
    ├── c_nme1_prod_200.rst
    ├── c_prod_200.out
    ├── c_rmsd.sh						# bash script for output structure backbone RMSD & RMSF
    ├── c_total_enegy.sh				# bash script for output total energy report file
    ├── nme1.solv.prmtop
    └── parameter
        ├── a_minimization_1.in
        ├── a_minimization_2.in
        ├── b_equilibrium_1.in
        ├── b_equilibrium_2.in
        ├── b_equilibrium_3.in
        ├── c_production_1.in
        ├── d_mmgbsa_com.in
        ├── d_mmgbsa_lig.in
        └── d_mmgbsa_rec.in