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. Author manuscript; available in PMC: 2019 May 31.
Published in final edited form as: J Phys Chem B. 2018 May 31;122(21):5466–5486. doi: 10.1021/acs.jpcb.7b11734

Figure 9. Phosphate-cation normalized fluctuation autocorrelation functions for binary occupancies around a DNA palindrome.

Figure 9.

The Drew-Dickerson DNA dodecamer (CGCGAATTGCGC) is a palindromic DNA sequence that has been traditionally been used as a demonstration of the slow convergence of ion distributions around the phosphate backbone of DNA. Phosphate-cation normalized fluctuation autocorrelation functions for binary occupancies in standard MD (thick green) and MD with dynamic ion sampling either neglecting the NCMC switching time (thick cyan), or the effective number of samples taken with accepted NCMC moves (dashed pink), or accounting for all NCMC MD steps whether the moves were accepted or not (dotted purple). The latter accounts for the total computational expense of our NCMC protocol. Shaded regions highlight 95% bootstrap confidence intervals, with bootstrap samples taken from all the adenine groups from the three simulations.