2.8. Molecular dynamic simulation

The docked complexes were subjected to MD simulation using Desmond module of Schrödinger software with OPLS 2005 force field. The protein–ligand complex was bounded with a predefined TIP3P water model (Jorgensen et al., 1983) in orthorhombic box. The volume of the box was minimized and the overall charge of the system was neutralized by adding Na⁺ and Cl^- ions. The temperature and pressure were kept constant at 310 Kelvin and 1.01325 bar using Nose–Hoover thermostat (Hoover, 1985) and Martyna–Tobias–Klein barostat (Zhong, 2004) methods. The simulations were performed using NPT ensemble by considering number of atoms, pressure and timescale. During simulations, the long–range electrostatic interactions were calculated using Particle–Mesh–Ewald method (Essmann et al., 1995). RMSD plots for the backbone atoms for both the protein and ligand bound protein were generated to decipher the relative stability of the ligand in the binding pocket of the M^pro. The results were analyzed and visualized by simulation interaction diagram and MS-MD trajectory analysis.