3.6.1.  Root mean square deviation (RMSD)
The RMSD values from MD simulation provide information about structural and conformational stability. Figure 5 represents the backbone RMSD data of viral proteins and their complex with Piperine. From the plot, it is observed that both the simulations have less fluctuation throughout the simulation time. The average RMSD values of RBD Spro, RBD Spro-Piperine, Mpro and Mpro-Piperine are calculated as 0.143 ± 0.025 nm, 0.130 ± 0.018 nm, 0.212 ± 0.041 nm and 0.203 ± 0.028 nm, respectively. The average RMSD values of the Piperine bound proteins as compared to only proteins are found to be less representing to their conformational stability. Both the simulations are attained equilibrium within 0.3 nm, which is also a measure of the systems’ stability during the simulation (Al-Shabib et al., 2018, 2020; Millan et al., 2018).
Figure 5.  Root mean square deviation plots of (a) RBD Spro (black) and RBD Spro-Piperine (red); (b) Mpro (black) and Mpro-Piperine (blue).