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Dynamic force matching: A method for constructing dynamical coarse-grained models with realistic time dependence.

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      Abstract

      Coarse-grained (CG) models of molecular systems, with fewer mechanical degrees of freedom than an all-atom model, are used extensively in chemical physics. It is generally accepted that a coarse-grained model that accurately describes equilibrium structural properties (as a result of having a well constructed CG potential energy function) does not necessarily exhibit appropriate dynamical behavior when simulated using conservative Hamiltonian dynamics for the CG degrees of freedom on the CG potential energy surface. Attempts to develop accurate CG dynamic models usually focus on replacing Hamiltonian motion by stochastic but Markovian dynamics on that surface, such as Langevin or Brownian dynamics. However, depending on the nature of the system and the extent of the coarse-graining, a Markovian dynamics for the CG degrees of freedom may not be appropriate. In this paper, we consider the problem of constructing dynamic CG models within the context of the Multi-Scale Coarse-graining (MS-CG) method of Voth and coworkers. We propose a method of converting a MS-CG model into a dynamic CG model by adding degrees of freedom to it in the form of a small number of fictitious particles that interact with the CG degrees of freedom in simple ways and that are subject to Langevin forces. The dynamic models are members of a class of nonlinear systems interacting with special heat baths that were studied by Zwanzig [J. Stat. Phys. 9, 215 (1973)]. The properties of the fictitious particles can be inferred from analysis of the dynamics of all-atom simulations of the system of interest. This is analogous to the fact that the MS-CG method generates the CG potential from analysis of equilibrium structures observed in all-atom simulation data. The dynamic models generate a non-Markovian dynamics for the CG degrees of freedom, but they can be easily simulated using standard molecular dynamics programs. We present tests of this method on a series of simple examples that demonstrate that the method provides realistic dynamical CG models that have non-Markovian or close to Markovian behavior that is consistent with the actual dynamical behavior of the all-atom system used to construct the CG model. Both the construction and the simulation of such a dynamic CG model have computational requirements that are similar to those of the corresponding MS-CG model and are good candidates for CG modeling of very large systems.

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      Most cited references 60

      • Record: found
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      • Article: not found

      Fast Parallel Algorithms for Short-Range Molecular Dynamics

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        • Record: found
        • Abstract: not found
        • Article: not found

        The missing term in effective pair potentials

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          • Record: found
          • Abstract: not found
          • Article: not found

          Transport, Collective Motion, and Brownian Motion

           Hazime Mori (1965)
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            Author and article information

            Affiliations
            [1 ] Department of Chemistry, The James Franck Institute, Institute for Biophysical Dynamics, and Computation Institute, The University of Chicago, Chicago, Illinois 60637, USA.
            [2 ] Department of Chemistry, Stanford University, Stanford, California 94305, USA.
            Journal
            J Chem Phys
            The Journal of chemical physics
            AIP Publishing
            1089-7690
            0021-9606
            Apr 21 2015
            : 142
            : 15
            25903863
            10.1063/1.4917454

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