Supplementary Figure 4: R.m.s. deviation (r.m.s.d.) and cross-correlation coefficient (CCC) plots of the MDFF process.
From: EttA regulates translation by binding the ribosomal E site and restricting ribosome-tRNA dynamics
(a) CCC plotted versus the simulation time in picoseconds (ps). (b) RMSD plotted versus the simulation time in picoseconds. In both (a) and (b), the MDFF equilibration phase (left plot) is distinct from the production phase (right plot). Dotted red lines separate consecutive stages of the equilibration phase conducted at decreasing positional harmonic constraints (in kcal/(mol*Å) at the top of the plots). The solid red line denotes the frame at which the convergence is considered achieved as it marks the beginning of a plateau.
