2.4.5. Molecular Dynamics

To evaluate the stability in a time of the ligand–albumin complexes, some molecular dynamics simulations were performed with GROMACS 2023 [33] using the CHARMM36 force field [34] on a machine running Debian 11. The computer has an Intel Core 7700 K CPU and an NVIDIA RTX 3060 GPU. Their interoperability was based on CUDA 12. Lig-ands parametrization was made using the CgenFF server [34].

The protein and the ligands were placed in an orthorhombic box with a 1 nm gap at the sides and were filled using the TIP3P solvation water model [35]. The preparation of the systems and running of the simulations were made according to the previous works reported [36–38]. Briefly, the main parameters used for carrying out molecular dynamics studies will be presented. The constructed systems were neutralized by adding sodium ions. The energy of the systems was minimized for 5000 steps using the steepest descent method, and the convergence was reached until the maximum force <1000 KJ mol−<sup>1</sup> ·nm−<sup>1</sup> to remove the steric clashes. The equilibration of the systems was made at NVT and NPT ensembles at 300 K for 100 ps (50,000 steps × 2 fs) each. The production of the simulations was run for 100 ns (50,000,000 × 2 fs) at 300 K and 1 bar with periodic boundary conditions on all axes.

Visualization of the evolution in time of the ligand–albumin complexes during the molecular dynamics simulation was made using VMD 1.9.4 [39].
