Figure 6.

Combined internal coordinate and Cartesian relax is more effective than either one alone. A representative set of starting models was relaxed using different protocols (colors) and the average energy over all calculations (y-axis) was determined as a function of run time (x-axis). At 200 s (black vertical bar), the minimization method within the relax protocol was changed as indicated in the inset box (for example, ideal-Cartesian indicates that the first 200 s used ideal bond internal coordinate minimization, and the second 200 s, Cartesian minimization (all DOFs variable). The best performance (lowest energies after 400 s) was obtained using protocols that kept bond lengths fixed in the first phase and switched to Cartesian minimization in the second phase.