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      Computing the non-Markovian coarse-grained interactions derived from the Mori–Zwanzig formalism in molecular systems: Application to polymer melts

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      The Journal of Chemical Physics
      AIP Publishing

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          Statistical Mechanics of Dissipative Particle Dynamics

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            Deriving effective mesoscale potentials from atomistic simulations.

            We demonstrate how an iterative method for potential inversion from distribution functions developed for simple liquid systems can be generalized to polymer systems. It uses the differences in the potentials of mean force between the distribution functions generated from a guessed potential and the true distribution functions to improve the effective potential successively. The optimization algorithm is very powerful: convergence is reached for every trial function in few iterations. As an extensive test case we coarse-grained an atomistic all-atom model of polyisoprene (PI) using a 13:1 reduction of the degrees of freedom. This procedure was performed for PI solutions as well as for a PI melt. Comparisons of the obtained force fields are drawn. They prove that it is not possible to use a single force field for different concentration regimes. Copyright 2003 Wiley Periodicals, Inc.
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              A multiscale coarse-graining method for biomolecular systems.

              A new approach is presented for obtaining coarse-grained (CG) force fields from fully atomistic molecular dynamics (MD) trajectories. The method is demonstrated by applying it to derive a CG model for the dimyristoylphosphatidylcholine (DMPC) lipid bilayer. The coarse-graining of the interparticle force field is accomplished by an application of a force-matching procedure to the force data obtained from an explicit atomistic MD simulation of the biomolecular system of interest. Hence, the method is termed a "multiscale" CG (MS-CG) approach in which explicit atomistic-level forces are propagated upward in scale to the coarse-grained level. The CG sites in the lipid bilayer application were associated with the centers-of-mass of atomic groups because of the simplicity in the evaluation of the forces acting on them from the atomistic data. The resulting CG lipid bilayer model is shown to accurately reproduce the structural properties of the phospholipid bilayer.
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                Author and article information

                Journal
                JCPSA6
                The Journal of Chemical Physics
                J. Chem. Phys.
                AIP Publishing
                0021-9606
                1089-7690
                January 07 2017
                January 07 2017
                : 146
                : 1
                : 014104
                Article
                10.1063/1.4973347
                28063444
                ada44f10-8de8-4299-8741-e32f0a2d03b2
                © 2017
                History

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