Explicit-solvent molecular dynamics simulations of a DNA tetradecanucleotide duplex: lattice-sum versus reaction-field electrostatics

Five long-timescale ( 10 ns) explicit-solvent molecular dynamics simulations of a DNA tetradecanucleotide dimer are performed using the GROMOS 45A4 force field and the simple-point-charge water model, in order to investigate the effect of the treatment of long-range electrostatic interactions as well as of the box shape and size on the structure and dynamics of the molecule ( starting from an idealised B-DNA conformation). Long-range electrostatic interactions are handled using either a lattice-sum (LS) method (particle-particle-particle-mesh; one simulation performed within a cubic box) or a cutoff-based reaction-field (RF) method ( four simulations, with long-range cutoff distances of 1.4 or 2.0 nm and performed within cubic or truncated octahedral periodic boxes). The overall double-helical structure, including Watson-Crick ( WC) base-pairing, is well conserved in the simulation employing the LS scheme. In contrast, the WC base-pairing is nearly completely disrupted in the four simulations employing the RF scheme. These four simulations result in highly distorted compact ( cutoff distance of 1.4 nm) or extended ( cutoff distance of 2 nm) structures, irrespective of the shape and size of the computational box. These differences observed between the two schemes seem correlated with large differences in the radial distribution function between charged entities ( backbone phosphate groups and sodium counterions) within the system.