Heat maps of all-to-all RMSD calculations show sampling of conformational substates during MD simulations. Transmembrane Cα atoms in mtre1, msctt, gtre1 and gsctt model systems were used in these calculations. The all-to-all RMSD calculation computes the RMSD of all pairs of frames in a trajectory. This all-to-all RMSD calculation was performed using the VMD plug-in RMSD Trajectory Tool . The RMSD scale is different for each model system and is located to the right of each plot.