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      Computing spatially resolved rotational hydration entropies from atomistic simulations

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          Abstract

          For a first principles understanding of macromolecular processes, a quantitative understanding of the underlying free energy landscape and in particular its entropy contribution is crucial. The stability of biomolecules, such as proteins, is governed by the hydrophobic effect, which arises from competing enthalpic and entropic contributions to the free energy of the solvent shell. While molecular dynamics simulations have revealed much insight, solvation shell entropies are notoriously difficult to calculate, especially when spatial resolution is required. Here, we present a method that allows for the computation of spatially resolved rotational solvent entropies via a non-parametric k-nearest-neighbor density estimator. We validated our method using analytic test distributions and applied it to an atomistic simulation of a water box. With an accuracy of better than 9.6%, the obtained spatial resolution should shed new light on the hydrophobic effect and the thermodynamics of solvation in general.

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          Most cited references30

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          Avoiding singularities and numerical instabilities in free energy calculations based on molecular simulations

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            The two-phase model for calculating thermodynamic properties of liquids from molecular dynamics: Validation for the phase diagram of Lennard-Jones fluids

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              Metrics for 3D Rotations: Comparison and Analysis

              Du Huynh (2009)
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                Author and article information

                Journal
                16 September 2019
                Article
                1909.07320
                093c4586-41c9-49a9-8964-f72a94c32f8a

                http://arxiv.org/licenses/nonexclusive-distrib/1.0/

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                Custom metadata
                physics.bio-ph physics.chem-ph physics.comp-ph stat.CO

                Mathematical & Computational physics,Physical chemistry,Biophysics,Mathematical modeling & Computation

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