#. make_reference_structure.py
   
#. make_init_md_traj.py
   
#. get_IC_md.py
   
#. learn_im_parameters.py

#. make_im_system.py

#. run_im_NVT_sampling.py

#. plot_bad_hist_im.py

#. compute_rmsd_centers_and_k_for_imus.py   

#. run_im_umbrella_sampling.py via submit_im_umbrella_sampling.sh

#. plot_rmsd_imus.py

#. compute_log_q_imus.py   
   
#. compute_basis_for_angles_and_dihedrals.py

#. compute_basis_rmsds.py

#. compute_elec_energy.py

#. compute_LJ_basis.py
   
#. contrastive_learning.py via submit_contrastive_learning.slm

#. make_full_system.py

#. run_full_NVT_sampling.py via submit_full_NVT_sampling.sh
   
