Accurate DNA dynamics without accurate long-range electrostatics

Molecular dynamics (MD) simulations of the DNA dodecamer d(CGCGAATTCGCG)(2), with the bulk solvent represented implicitly but the minor groove filled with explicit water, demonstrate the excellent stability of both the duplex in B form and the water shell and converge to the same final state starting from different initial conformations. This opens the way to MD simulations of much longer sequences. The final state appears surprisingly close to the experimental B-DNA structures, much closer than in earlier, more expensive simulations involving explicit counterions, periodic boundary conditions, and particle mesh Ewald evaluations of Coulomb forces. This paper presents the first application of a new internal coordinate molecular dynamics (ICMD) method to nucleic acids. Two ICMD trajectories computed with a 10-fs time step exhibit the same qualitative features and converge to the same structure as the traditional Cartesian coordinate MD.