Figure 2.

Relationship between computational time and structure size for different algorithms used in the GNM analysis. The computational times (seconds) are plotted on a log-log scale against the number N of residues for 13 test proteins. The amount of time required to calculate all the GNM modes and theoretical B-factors (B^GNM) by the standard SVD approach (black circles) scales as t_SVD = 2.2 × 10⁻⁸ N^3.30. The PowerB calculation (blue diamonds) scales as t_Power = 7.2 × 10⁻⁶ N^2.04. The computation of the 101 slowest modes using BLZPACK (red squares) exhibits a power law of t_BLZP = 5.9 × 10⁻² N^0.49. Using the latter two methods sequentially results in a dramatic decrease in computing time without loss of accuracy. The improvement is especially significant for large structures (N > 2000), permitting us to release on-line results in oGNM.