Well-structured regions and loosely bound regions in proteins and nucleic acid strands are distinguished by low and high root mean square fluctuations values respectively . RMSF also records the fluctuation of each amino acid base pair including the fluctuations in the flexible regions within the nucleic acid during the course of the MD simulation. For small proteins, a fluctuation between 1~3 Å is acceptable . The graph shown below in figure suggests that complex-2 had the least fluctuations in its residues from beginning till the end of the simulations, and hence claims to be the most stable complex.