Abstract
We present a novel approach for the selection of DNA step parameters as reaction coordinates in umbrella sampling simulations. Simplified representation of DNA that uses only three atoms per base, allowed for highly efficient calculations of the step parameters and their Cartesian derivatives in the molecular dynamics simulations. Good correlation between the actual and calculated twist, roll, tilt, rise, slide and shift was obtained. The method is illustrated through its application to the unmethylated and methylated DNA systems. Impact of the methylation on the shape and flexibility of DNA depending on the location of the methyl group is discussed.
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