title: Molecular dynamics simulations of double-stranded DNA in an explicit solvent model with the zero-dipole summation method.
abstract: Molecular dynamics (MD) simulations of a double-stranded DNA with explicit water and small ions were performed with the zero-dipole summation (ZD) method, which was recently developed as one of the non-Ewald methods. Double-stranded DNA is highly charged and polar, with phosphate groups in its backbone and their counterions, and thus precise treatment for the long-range electrostatic interactions is always required to maintain the stable and native double-stranded form. A simple truncation method deforms it profoundly. On the contrary, the ZD method, which considers the neutralities of charges and dipoles in a truncated subset, well reproduced the electrostatic energies of the DNA system calculated by the Ewald method. The MD simulations using the ZD method provided a stable DNA system, with similar structures and dynamic properties to those produced by the conventional Particle mesh Ewald method.
authors.affiliation: Institute for Protein Research, Osaka University, Suita, Osaka, Japan.
authors.forename: Takamasa
authors.initials: T
authors.lastname: Arakawa
authors.forename: Narutoshi
authors.initials: N
authors.lastname: Kamiya
authors.forename: Haruki
authors.initials: H
authors.lastname: Nakamura
authors.forename: Ikuo
authors.initials: I
authors.lastname: Fukuda
mesh_terms: D000465:Algorithms; D004247:DNA / Q000737:chemistry*; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D009690:Nucleic Acid Conformation; D012997:Solvents; D055672:Static Electricity
chemical_list: D012997:Solvents; D004247:DNA