5.10. Molecular Dynamics Simulations

The molecular docking simulations were followed by molecular dynamic (MD) simulations using the Desmond package. MD simulations were performed to identify the effectiveness of saroglitazar against EGFR⁶⁸ and modulation using the SPC water model. All the systems were subjected to energy minimization, and the systems were placed in the cubic box with a buffered distance of 10 Å for the generation of a hydration model. Finally, the MD simulations were performed under the NPT ensemble for 10 ns. For the validation of the molecular dynamic simulation, a 100 ns MD simulation were performed and graphs values were collected to extract the graphs of root-mean-square deviations (RMSD) and root-mean-square fluctuations (RMSFs). The graphs were plotted using raw data obtained from DESMONDs and MS excel. The trajectories of MD simulation were analyzed through simulation event analysis, simulation quality analysis, which were then further studied in the Simulation Interaction Diagram tool in Maestro.