RMSF

RMSF, short for root mean square fluctuation, is a metric used in molecular dynamics and structural biology to quantify the mobility of atoms or residues over the course of a simulation. For a given atom i, RMSF is computed from a trajectory of length T as RMSF(i) = sqrt( (1/T) sum_{t=1}^T [ r_i(t) - <r_i> ]^2 ), where r_i(t) is the position of atom i at time t and <r_i> is its time-averaged position across the trajectory. In practice, RMSF is often calculated for the Cα atoms of residues, or for all heavy atoms within a residue, after aligning all frames to a reference structure to remove overall translation and rotation.

Interpretation and use: Higher RMSF values indicate greater positional fluctuations and thus higher local flexibility, while lower values indicate rigidity. RMSF is commonly used to map the dynamic landscape of a protein, highlighting flexible loops, hinges, or binding regions. It is also employed to compare different states, such as wild-type versus mutant proteins, or structures under different temperatures or ligand-binding conditions.

Computation considerations: The reliability of RMSF depends on adequate sampling and trajectory length, as well as the choice of atoms used in the calculation and the alignment protocol. Periodic boundary conditions and the handling of solvent can influence results. RMSF is related to, but distinct from, RMSD (root mean square deviation); RMSD measures global structural deviation from a reference, while RMSF assesses fluctuations around mean positions over time.

Relation to experiments and other metrics: RMSF values often correlate with experimental B-factors from X-ray crystallography, reflecting atomic mobility, though differences in conditions and sampling must be considered.