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      Modeling real dynamics in the coarse-grained representation of condensed phase systems.

      1 ,
      The Journal of chemical physics
      AIP Publishing

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          Abstract

          This work presents a systematic multiscale methodology to provide a more faithful representation of real dynamics in coarse-grained molecular simulation models. The theoretical formalism is based on the recently developed multiscale coarse-graining (MS-CG) method [S. Izvekov and G. A. Voth, J. Phys. Chem. B. 109, 2469 (2005); J. Chem. Phys. 123, 134105 (2005)] and relies on the generalized Langevin equation approach and its simpler Langevin equation limit. The friction coefficients are determined in multiscale fashion from the underlying all-atom molecular dynamics simulations using force-velocity and velocity-velocity correlation functions for the coarse-grained sites. The diffusion properties in the resulting CG Brownian dynamics simulations are shown to be quite accurate. The time dependence of the velocity autocorrelation function is also well-reproduced relative to the all-atom model if sufficient resolution of the CG sites is implemented.

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          A Continued-Fraction Representation of the Time-Correlation Functions

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            Nonlinear generalized Langevin equations

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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
                J Chem Phys
                The Journal of chemical physics
                AIP Publishing
                0021-9606
                0021-9606
                Oct 21 2006
                : 125
                : 15
                Affiliations
                [1 ] Center for Biophysical Modeling and Simulation and Department of Chemistry, University of Utah, Salt Lake City, Utah 84112-0850, USA.
                Article
                10.1063/1.2360580
                17059230
                2817d64c-0fa7-45c3-a38f-190d45ae07b2
                History

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