Which is the most latest & efficiently best way of representing the RMSD & RMSF Plots of multiple complexes of MD Simulations of Protein-Ligand complexes ?
Several softwares are used for the efficient way to plot the RMSD, RMSF, rGyr, SASA, etc such as QTgrace, GraphPad, Sigma and most easy way used Excel.
Python scripts and the MDAnalysis library provide highly specialised options. The use of various graphics libraries with the MDAnalysis library can allow you to create both aesthetically and scientifically powerful graphics.