MODELING THE DNA-SOLVENT INTERFACE

We extend the technique of using perpendicular distribution functions to salt solutions around nucleic acids. Both solute density averaged a nd nonaveraged reference frames are considered and compared. Using a p revious simulation of DNA in salt water of over a nanosecond in durati on, the aqueous distribution functions were found to be well converged , whereas the salt perpendicular distribution functions were less well determined. Three-dimensional density reconstructions reliably showed the prominent solvation features with transferable functions. The num ber of solute atom types needed for reconstructions of a given precisi on was determined in the context of the reference simulation data set with the goal of achieving a required level of reconstruction quality. (C) 1997 John Wiley & Sons, Inc.