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. 2006 Oct 15;91(8):2976–2990. doi: 10.1529/biophysj.106.083667

FIGURE 1.

FIGURE 1

Time-series of the all-atom (non-mass-weighted) RMSD values from the initial (model) structure (including the 0.1 ns equilibration time; from −0.1 to 0.0 ns) together with the corresponding RMSF values (excluding a total of 0.2 ns equilibration time) for the MD simulations starting from B- or Z-DNA and the TMD simulations of the B-to-Z transition under different ionic-strength conditions. For the TMD simulations, the RMSD from the target (equilibrated) Z-DNA structure is also shown. The end structure of each simulation is shown on the right. Panel codes (see Table 1) correspond to a, B0; b, BN; c, BE; d, Z0; e, ZN; f, ZE; g, BZ0; h, BZN; and i, BZE.