The conformational stability was evaluated by RMSD analysis by calculating the RMSD data of alpha carbon atoms of the protein backbone for all the protein-inhibitor complexes and the unligated protein with respect to the initial structures. During MD simulation the system was heated to 300 K for 120 ps at first, then equilibrated for 1 ns and then went through production phase for 20 ns beginning at 1.12.ns. The average RMSD value for M Pro protein was found to be 0.170 ± 0.027 nm and for the M Profamotidine, M Pro -CNP0416047, M Pro -3 hydroxy anisotine, and M Pro -anisotine complexes were found to be 0.168 ± 0.028, 0.165 ± 0.021 nm, 0.181 ± 0.0175, 0.166 ± 0.030 proving the conformational stabilities of the protein-inhibitor complexes (Table ). The RMSD of the native protein slightly fluctuated between 0.9 nm to 0.16 nm for the first 5 ns period of time and remained between 0.15 to 0.21 nm for the rest (Figure ). The RMSD of M Pro -famotidine complex maintained a value of 0.10 -0.15 nm up to 5 ns and reached a plateau between 0.12 nm -0.20 nm after 5 ns with some fluctuation up to 0.26 nm at 11 ns. For M Pro -CNP0416047 complex, a plateau was reached after 5 ns with almost constant values between 0.16 nm to 0.19 nm. In case of M Pro -3 hydroxy anisotine complex, the RMSD curve became horizontal after almost 5.5 ns and the RMSD value was converged to 0.16 -0.20 nm. The RMSD curve of M Pro -anisotine complex showed horizontal nature for first 4 ns, but fluctuate in greater extent from 5 ns to 20 ns time period than the other complexes with ranges between 0.13 nm to 0.22 nm in that period.