We know that Root Mean Square Deviation (RMSD) and Root Mean Square Fluctuation (RMSF) are both common metrics used in the analysis of molecular dynamics (MD) simulations, particularly in the context of proteins. So what is the exact difference between these two analysis ?
RMSD (root mean square deviation) represents the deviation of a coordinate set from a reference set. In molecular dynamics, the reference set is represented by the starting point of the simulations and so the calculation of RMSD allows us to observe how these coordinates evolve with respect to the starting point.
On the other hand, RMSF (root mean square fluctuation) does not indicate positional differences in the time, but rather measures the individual flexibility of residues, thus how much a particular residue moves during a simulation.
So basically in MD you plot RMSD vs time and RMSF vs residue number!
Main difference is that r. m. s. d is conformational difference of whole protein molecule with respect to time in the MD trajectory while r. m. s. f is the total fluctuation of individual amino acid residues during entire period of simulation. (However, r. m. s. deviation can also be plotted for selective or specific region of protein with respect to time like r. m. s. d of backbone, side chain, particular region of an individual domain.) The r. m. s. d. graph is plotted against time while r. m. s. f. graph is plotted against sequence of residues. So, r. m. s. d shows deviation of overall protein molecule during simulation and indicates overall conformational stability whereas r. m. s. f plot shows conformational flexibility of individual region. Radius of gyration plot would complement the information about conformational stability.
Moreover, r. m. s. d plot are also being used as parameter to analyze the equilibration/convergence of MD simulation but not always. Sometime, r. m. s. d plot can mislead the information about convergence for proteins which shows greater flexibility like kinases.