title: Adaptive resolution simulation of a DNA molecule in salt solution.
abstract: We present a multiscale simulation of a DNA molecule in 1 M NaCl salt solution environment, employing the adaptive resolution simulation approach that allows the solvent molecules, i.e., water and ions, to change their resolution from atomistic to coarse-grained and vice versa adaptively on-the-fly. The region of high resolution moves together with the DNA center-of-mass so that the DNA itself is always modeled at high resolution. We show that our multiscale simulations yield a stable DNA-solution system, with statistical properties similar to those produced by the conventional all-atom molecular dynamics simulation. Special attention is given to the collective properties, such as the dielectric constant, as they provide a sensitive quality measure of our multiscale approach.
authors.affiliation: Laboratory for Molecular Modeling, National Institute of Chemistry , Hajdrihova 19, SI-1001 Ljubljana, Slovenia.
authors.forename: Julija
authors.initials: J
authors.lastname: Zavadlav
authors.affiliation: Department of Physics, Faculty of Mathematics and Physics, University of Ljubljana , Jadranska 19, SI-1000 Ljubljana, Slovenia.|Theoretical Physics Department, J. Stefan Institute , Jamova c. 39, SI-1000 Ljubljana, Slovenia.
authors.forename: Rudolf
authors.initials: R
authors.lastname: Podgornik
authors.affiliation: Laboratory for Molecular Modeling, National Institute of Chemistry , Hajdrihova 19, SI-1001 Ljubljana, Slovenia.
authors.forename: Matej
authors.initials: M
authors.lastname: Praprotnik
mesh_terms: D004247:DNA / Q000737:chemistry*; D056004:Molecular Dynamics Simulation; D012965:Sodium Chloride / Q000737:chemistry*; D012996:Solutions
chemical_list: D012996:Solutions; D012965:Sodium Chloride; D004247:DNA