Quantum mechanical calculations and molecular dynamics (MD) simulations have been used to obtain an accurate and time-averaged representation of the charge distribution of a DNA-water-Na+ system. Having derived a set of time-averaged charges for the phosphate and the sodium ions, two 150 ps MD simulations have been performed to obtain a more complete picture of the dynamic characteristics of the DNA, including solvent and counterion environment. In agreement with other theoretical approaches to the analysis of DNA/ion interaction, about 80% of the counterions are associated with the DNA. This occurs almost entirely through interaction with the phosphate groups, the counterions being distributed approximately equally between the first and second coordination shells of the phosphates. The revised partial charges for the phosphate group and sodium ion appear to result in structural parameters for the DNA which remain in somewhat better agreement with experimental data than when the standard charges are used.