RMSD (Root-Mean-Square Deviation)

Root-mean-square deviation quantifies the average positional difference, typically measured in Ångströms, between two superimposed sets of atomic...

Root-mean-square deviation quantifies the average positional difference, typically measured in Ångströms, between two superimposed sets of atomic coordinates, and serves two distinct but related purposes within structure-based drug design. In docking validation, RMSD measures the deviation between a computationally predicted ligand pose and the experimentally determined (co-crystallised) pose of the same ligand, with values below approximately 2.0 Å conventionally regarded as indicating a successful, near-native pose prediction. In molecular dynamics simulation, RMSD is tracked continuously over the simulation trajectory relative to the starting structure, providing a direct measure of overall structural stability, with a plateauing RMSD trace after an initial equilibration period taken as evidence that the simulated system has reached a stable conformational state.