Modeling diffusive dynamics in adaptive resolution simulation of liquid water

Abstract

We present a dual-resolution molecular dynamics (MD) simulation of liquid water employing a recently introduced Adaptive Resolution Scheme (AdResS). The spatially adaptive molecular resolution procedure allows for changing from a coarse-grained to an all-atom representation and vice versa on-the-fly. In order to find the most appropriate coarse-grained water model to be employed with AdResS, we first study the accuracy of different coarse-grained water models in reproducing the structural properties of the all-atom system. Typically, coarse-grained molecular models have a higher diffusion constant than the corresponding all-atom models due to the reduction in degrees of freedom (DOFs) upon coarse-graining that eliminates the fluctuating forces associated with those integrated-out molecular DOFs. Here, we introduce the methodology to obtain the same diffusional dynamics across different resolutions. We show that this approach leads to the correct description of the here relevant structural, thermodynamical, and dynamical properties, i.e., radial distribution functions, pressure, temperature, and diffusion, of liquid water at ambient conditions.

Transport properties controlled by a thermostat: An extended dissipative particle dynamics thermostat

“…The electrostatics is described by the reaction field (RF) method, in which all molecules outside a spherical cavity of a molecular based cutoff radius R c = 9Å are treated as a dielectric continuum with a dielectric constant ǫ RF = 80 39 with the friction constant ζ = 0.5ps −1 and cutoff radius R c . The constant ζ is small compared to the intrinsic friction coefficient ξ of the TIP3P water system, i.e., ξ = 288.6ps −1 , so that the stochastic dynamics yields the correct dynamics 29,51 . For the coarse-grained water simulations with the Transverse DPD thermostat we have employed the single-site water model from Ref.…”

Communication: On the locality of Hydrogen bond networks at hydrophobic interfaces

“…If adaptive resolution simulations with a minimal all-atom region can reproduce the results of fully all-atom simulations, then the effect of solute on the water structure is deemed local: it is not significantly supported/influenced by the bulk hydrogen bond network, as the bulk is modeled by CG water, unable to form directional hydrogen bonds. 12,13 In this case the role of the CG bulk water for the surface layer is minimal, that is, it is enough to ensure that the CG water acts as a thermodynamic bath with the same temperature, pressure, and density as the all-atom model. If the structural properties are perfectly local, there is no need for the CG bulk to provide any structural information.…”

Grand Canonical adaptive resolution simulation for molecules with electrons: A theoretical framework based on physical consistency

“…Despite its conceptual simplicity, this approach produced highly satisfactory results for a large variety of systems and physical situations [31][32][33][34][35][36][37][38]. However, exactly because it turned to be a numerically satisfactory approach, a deeper conceptual justification of the idea was mandatory.…”

“…there is the expected flux in both directions) and that the probability distribution of molecules in the quantum region, P (N ), follows the expected Gaussian behaviour. This is routinely done in AdResS while the simulation runs (see for example [33,60,61]). If both criteria are fulfilled, automatically we have exchange of molecules at the correct chemical potential.…”