Fig. 4: Dynamic characteristics in equilibrium.

a Schematics of the 12-helix-bundle (12HB) structure. The helix index denotes the straight helices in a honeycomb lattice, and the base-pair index indicates the node in a helix from one end to the other. The configuration represents the final snapshot of the structure. b RMSD profiles in the simulation. We performed the analysis using the proposed method, oxDNA¹¹, and mrDNA¹⁴ for the comparison with the MD results³⁴. c Root-mean-square fluctuation (RMSF) amplitudes. For each approach, the RMSF profile and its normalized histogram as a probability density function (PDF) are shown. d Correlation maps. Pearson and generalized correlations were calculated using the final 20-ns-long trajectories. The enlarged plots demonstrate the correlations between two adjacent helices connected by five crossover sites (helix index: 2 and 11). e Normalized histograms of the correlation maps. The vectorized difference in the Pearson and generalized correlation maps between MD and the other approaches was used to draw the probability density function. The difference value was calculated as \({\vec{{{{{{\rm{c}}}}}}}}_{{{{{{\rm{MD}}}}}}}-\vec{{{{{{\rm{c}}}}}}}\) where \({\vec{{{{{{\rm{c}}}}}}}}_{{{{{{\rm{MD}}}}}}}\) and \(\vec{{{{{{\rm{c}}}}}}}\) represent vectorized correlation values obtained from MD and other methods, respectively.