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. Author manuscript; available in PMC: 2015 Jun 15.
Published in final edited form as: J Comput Chem. 2014 Apr 18;35(16):1219–1239. doi: 10.1002/jcc.23611

Figure 5.

Figure 5

Time series from EcoR1 Drude MD simulation for (A) sugar puckering of strand 1, nucleotide 3, (B) ε of strand 1, nucleotide 4, and (C) ζ of strand 1, nucleotide 4. Data points are shown for every 50 ps. In the BI state ε and ζ are approximately 190° and 270°, respectively, and in the BII state they are approximately 270° and 180°, respectively. The pseudorotation angle characterizing the conformation of the sugar moiety assumes values of approximately 175° and 15° when the sugar is in the south and north states, respectively.