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  • Title: Multiscale coarse-graining of monosaccharides.
    Author: Liu P, Izvekov S, Voth GA.
    Journal: J Phys Chem B; 2007 Oct 04; 111(39):11566-75. PubMed ID: 17850132.
    Abstract:
    A systematic multiscale coarse-graining (MS-CG) algorithm is applied to build coarse-grained models for monosaccharides in aqueous solution. The methodology is demonstrated for the example of alpha-D-glucopyranose. The nonbonded interactions are directly derived from the force-matching approach, whereas the bonded interactions are obtained through Boltzmann statistical analyses of the underlying atomistic trajectory. The MS-CG model is shown to reproduce many structural and thermodynamic properties in the constant NPT ensemble. Although the model is derived at a single temperature, pressure, and concentration, it is shown to be reasonably transferable to other thermodynamic states. In this model, long-range interactions are effectively mapped into short-range forces with a moderate cutoff and are evaluated by table look-up. As a result, molecular dynamics employing the MS-CG model is approximately 3 orders of magnitude more efficient than its atomistic counterpart. Consequently, the model is particularly suitable for simulating carbohydrate systems at large length and long time scales. Results for an alpha-(1-->4)-d-glucan with 14 glucose units are also presented, demonstrating that the MS-CG algorithm is also applicable to the coarse-graining of other saccharide systems.
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