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.
Rudnicki
W R
WR
Interdisciplinary Centre for Mathematical and Computational Modeling Warsaw University, Poland.
Pettitt
B M
BM
D003198:Computer Simulation; D004247:DNA / Q000737:chemistry*; D008956:Models, Chemical; D012996:Solutions / Q000737:chemistry*; D014867:Water / Q000737:chemistry*
D012996:Solutions; D014867:Water; D004247:DNA