Application of the RISM method to estimate the relative gibbs free energies of 4${}'$,6-diamidino-2-phenylindole binding within the minor groove of a DNA along simulation trajectory

The efficient parallel algorithm for solving RISM equations in infinity dilution limit and estimate of solvation free energy was applied to study the relative binding energies of sequence-specific binding modes of 4${}'$,6-diamidino-2-phenylindole (DAPI) within the minor groove of a DNA duplex. The speedy implementation allows solvation free energies to be calculated at all points along a given simulation trajectory, leading to a more accurate representation of the solute than in the usual RISM approach considering the solute molecule as frozen.