Fig. 2.

Average fluctuations and correlated motions. (A) Time-averaged (excluding the first 5 ns) simulation C^α B factors compared with experimental (i.e., x-ray) B factors. The x-ray B factors are shown as a gray line; the simulation B factors obtained by averaging the four simulation B-factor curves for the individual chains are shown as a broken line; and the simulation B factors derived from a trajectory composed of the average structure of all four OmpA chains at each point in time are shown as a solid black line. (B) Schematic “porcupine plot” diagram of the first principal component of the simulated motion of OmpA chain C (shown in C^α trace format). The cones represent fluctuations, with their orientation indicating the direction of motion of the C^α atom to which they are attached and their length indicating the amplitude of this motion. The figure was made by using dynamite (21).