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 essential thermodynamic, structural and dynamical properties of liquid water at ambient conditions.

12 pages, 16 figures

References in corpus (10)

• Protein folding mediated by solvation: water expelling and formation of the hydrophobic core occurs after the structure collapse
• Adaptive Resolution Molecular Dynamics Simulation: Changing the Degrees of Freedom on the Fly
• Representability problems for coarse-grained water potentials
• Resolution exchange simulation
• Adaptive Resolution Simulation of Liquid Water
• Multiscale modelling of liquids with molecular specificity
• A Macromolecule in a Solvent: Adaptive Resolution Molecular Dynamics Simulation
• Some fundamental problems for an energy conserving adaptive resolution molecular dynamics scheme
• Adaptive molecular resolution via a continuous change of the phase space dimensionality
• Dissipating the Langevin equation in the presence of an external stochastic potential

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