Modeling the DNA-solvent interface

We extend the technique of using perpendicular distribution functions to salt solutions around nucleic acids. Both solute density averaged and nonaveraged reference frames are considered and compared. Using a previous simulation of DNA in salt water of over a nanosecond in duration, the aqueous distribution functions were found to be well coveraged, whereas the salt perpendicular distribution functions were less well determined. Three-dimensional density reconstructions reliably showed the prominent solvation features with transferable functions. The number of solute atom types needed for reconstructions of a given precision was determined in the context of the reference simulation data set with the goal of achieving a required level of reconstruction quality.