FIGURE 2.

(A) RMSD relative to the crystal structure for L11–rRNA complex, ribosomal RNA, and L11. The dashed line separates the first nanosecond, in which equilibration occurs, from the last 15 nsec of the simulation. (B) Average fluctuations of Cα and phosphate atoms throughout the trajectory. Five peaks occur in the RNA, which are labeled from P1 to P5.