The next step involves the energy minimization of the trypsinbenzamidine complex to its local minima, followed by equilibration in the NVT ensemble. System minimization aims to find an energetically stable conformation of the system by iteratively adjusting the atomic positions to minimize the potential energy, therefore beginning with a favorable starting structure. Equilibration prepares the biomolecular complexes for MD production runs by resolving initial structural and energetic irregularities, ensuring stable and reliable simulations under target conditions. To perform the energy minimization followed by system equilibration, we execute the following command in the terminal: python minimize_equilibriate.py