The impact of monovalent ion force field model in nucleic acids simulations.
Different classical models for monovalent ions (typically used to neutralize proteins or nucleic acids) are available in the literature and are widely used in molecular dynamics simulations without a great knowledge of their quality, consistency with the macromolecular force field and impact on the global simulation results. In this paper the ability of several of the most popular ion models to reproduce both quantum mechanics and experimental results is examined. Artefacts due to the use of incorrect ion models in molecular dynamics simulations of concentrated solutions of NaCl and KCl in water and of a short DNA duplex in 500 mM aqueous solutions of NaCl and KCl have been analyzed. Our results allow us to discuss the robustness and reliability of different ion models and to highlight the source of potential errors arising from non-optimal models. However, it is also found that the structural and dynamic characteristics of DNA (as an example of a heavily charged macromolecule) in near-physiological conditions are quite independent of the ion model used, providing support to most already-published simulations of macromolecules.
Noy
Agnes
A
Department of Physics and Astronomy, University of Sheffield, Sheffield, UK S3 7RH.
Soteras
Ignacio
I
Luque
F Javier
FJ
Orozco
Modesto
M
D004247:DNA / Q000737:chemistry*; D007477:Ions / Q000737:chemistry; D056004:Molecular Dynamics Simulation; D009690:Nucleic Acid Conformation; D011189:Potassium Chloride / Q000737:chemistry; D011789:Quantum Theory; D012965:Sodium Chloride / Q000737:chemistry; D013816:Thermodynamics; D014867:Water / Q000737:chemistry
D007477:Ions; D014867:Water; D012965:Sodium Chloride; D011189:Potassium Chloride; D004247:DNA