The impact of monovalent ion force field model in nucleic acids simulations

Abstract

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.

A coarse-grain three-site-per-nucleotide model for DNA with explicit ions

“…For the sake of completeness, the RDF predicted by 3SPN.1-I is compared to all force fields investigated in Ref. 42. The local structure exhibited by 3SPN.1-I is well within the range of all force fields presented in that work.…”

“…The coarse-grain Na + -Cl − potential presented in this work is compared to the Na + -Cl − PMFs resulting from the force fields reviewed in Ref. 42 in Figure 2. The coarse-grain RDFs determined from the production run described earlier for the ion pairs Na + -Cl − , Na + -Na + , and Cl − -Cl − are shown in Figure 4(a) and the Na + -Cl − RDF is compared to the review of Noy et al in Figure 3.…”

“…We chose Na + -Cl − parameters to correspond to the Roux PMF. In the limiting case 42 for Na + -Cl − . The data are separated into two panels for ease of comparison.…”

“…42 We rely on their results to parameterize Na + -Cl − interactions. Noy et al limited their study to To determine the local structure exhibited by Mg 2 + and Cl − in aqueous solution an all-atom simulation was performed using the AMBER99 force field 43 in GROMACS.…”

“…For the Na + -Cl − interaction, the results of Noy et al 42 were used to determine the parameters for the coarse-grain potential. Noy et al determined the potential of mean force (PMF) between two isolated ions (Na + and Cl − ) in water at 298 K for a number of common force fields.…”