Molecular dynamics simulation studies of a high resolution Z-DNA crystal

We report two 1 ns molecular dynamic (MD) simulations on Z-DNA for which the long-range Coulomb terms are explicitly evaluated by the Particle–Mesh–Ewald method [J. Chem. Phys. 98, 10089 (1993)]. The starting structures were based on the 1 Å resolution crystallographic structure of Gessner et al. [J. Bio. Chem. 264, 7921 (1989)]. The average simulation structures of the DNA compare well to the crystallographic structure; the root-mean-square position deviations for the DNA double-strand heavy atoms are approximately 0.5 Å. Watson–Crick hydrogen bonding patterns are preserved without invoking constraints. These results emphasize the importance of proper treatment of the long-range forces for highly ionic systems.