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Optimal configurations of the systems B1–B4 found according to the scheme of rigid body replica exchange method followed by ca. 50 ns of unbiased calculations in NPT ensemble. Each iM molecule is displayed in different color in order to make the presentation clearer, DOX is shown as yellow spheres. The +/− DOX and +/− H(+) arrows inform which change of the system state is done, i.e., incorporation/removal of DOX, application of protonated/unprotonated iM.
