Additionally, the solvent accessibility surface area (SASA) was also computed to examine the solvent attributable areas of all simulation system. The cluster analysis having a cut-off value of 0.25 and 0.2 nm for spike protein and main protease respectively, depending upon the RMSD profile were utilized to demonstrate the conformations found utmost intermittently throughout the trajectory. Here, all the structures having RMSD values of below 0.25 nm for all components within a cluster are incorporated to the initial cluster. It is rare that a molecule having a higher value for RMSD than 0.25 nm from other cluster supposedly would be treated as a structure. The secondary structure analysis was also performed using the DSSP program (Martin et al., 2005). The visualization of protein nature during the entire simulation was accomplished by using Visual Molecular Dynamics (VMD) (Humphrey et al., 1996) and UCSF Chimera (Pettersen et al., 2004).