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. 2012 Aug 22;103(4):767–776. doi: 10.1016/j.bpj.2012.06.024

Figure 2.

Figure 2

Large-scale testing of QM/DMD: structure recapitulation and recovery for reduced rubredoxin. (A) The QM-DMD region RMSD from the x-ray structure (light green lines), the QM energies (pink lines), and the DMD energies (light purple lines) stabilize by the fifth iteration. Thick lines illustrate the return of the distorted WT structure to equilibrium in terms of the QM-DMD region RMSD (green), QM energy (red), and DMD energy (purple). (B) The overlay of the x-ray structure (light blue) and the distorted structure (pink), and of representative QM-DMD equilibrated structures, starting from x-ray (dark blue) and from the distorted structure (red).