Adaptive resolution simulation of salt solutions

Abstract

We present an adaptive resolution simulation of aqueous salt (NaCl) solutions at ambient conditions using the adaptive resolution scheme. Our multiscale approach concurrently couples the atomistic and coarse-grained models of the aqueous NaCl, where water molecules and ions change their resolution while moving from one resolution domain to the other. We employ standard extended simple point charge (SPC/E) and simple point charge (SPC) water models in combination with AMBER and GROMOS force fields for ion interactions in the atomistic domain. Electrostatics in our model are described by the generalized reaction field method. The effective interactions for water-water and water-ion interactions in the coarse-grained model are derived using structurebased coarse-graining approach while the Coulomb interactions between ions are appropriately screened. To ensure an even distribution of water molecules and ions across the simulation box we employ thermodynamic forces. We demonstrate that the equilibrium structural, e.g. radial distribution functions and density distributions of all the species, and dynamical properties are correctly reproduced 4

Adaptive resolution simulation of an atomistic DNA molecule in MARTINI salt solution

“…In accordance with previous studies [51,58] we find that smoother NDPs are achieved when the TD forces are slightly extended into the AT and CG regions. Here, we apply the TD force in the range r AT −r skin < r < r HY +r skin , where r skin = 0.3 nm is the extension and r AT = 2.1 nm and r HY = 3.3 nm are the radii of the AT and HY domains, respectively.…”

“…The force acts on the CoM in the HY region and depends on the type of the entity. Therefore, we calculate three different forces that correspond to water bundles and Na + and Cl − ions [51]. The simulation setup and protocol are similar as in our previous work [38].…”

“…This can be observed from the NDPs of AdResS simulation where the TD force is acting only on bundles. In contrast, both Na + and Cl − TD forces have to be iterated simultaneously, since the density distributions of Na + and Cl − are mutually dependent [51]. The positional ion-ion, and water-ion, and water-water correlations are characterized by the corresponding radial distribution functions (RDFs), which are shown in Fig.…”

Molecular Dynamics Simulation of High Density DNA Arrays

“…Better agreement with the experiments was found for the Joung and Cheatham salt parameters [106], chosen such as to reproduce the relevant experimental osmotic pressure of DNA arrays [53]. In the context of AdResS, where any two AT and CG salt solution models can be coupled, the structure-based coarse-graining approaches, i.e., the Iterative Boltzmann Inversion method [96] that is incorporated into the STOCK web toolkit [68,107], are more convenient, as they allow a direct structural comparison with the underlying AT model.…”

“…Only recently it became feasible to set up an all-atom MD simulation for a larger set of DNA molecules [51,53] characterized by a single packing geometry with only a partial characterization of the DNA countercharge and solvent ordering. This approach has been later extended by the applications of the multiscale MD technique AdResS (Adaptive Resolution Scheme) [54][55][56][57][58][59][60][61][62][63][64][65][66][67], which has been already successfully applied to various biological systems [68][69][70][71][72][73][74][75][76][77], enabling a concurrent and consistent coupling between the atomistic (AT) and the coarse-grained (CG) representations with a key feature of allowing molecules to freely move not only in real space but also in the resolution space across different regions and change their resolution on the fly according to their position in the computational domain.…”