Molecular Dynamics Simulations on Solvated Biomolecular Systems: The Particle Mesh Ewald Method Leads to Stable Trajectories of DNA, RNA, and Proteins

This communication presents results from molecular dynamics (MD) simulations with AMBER 4.1 and the Cornell et al. force field of three different, fully solvated, fully charged, macromolecular structures: X-ray-derived structures of d(C-CAACGTTGG) sub(2) DNA and ubiquitin and an NMR-derived r(UUCG) RNA hairpin loop and stem structure. We compare the use of the particle mesh Ewald (PME) method for the treatment of long-range electrostatic interactions to standard charge group based truncation cutoff (CUT) methods used in simulations with periodic boundary conditions.