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    Rapid Exploration of Configuration Space with Diffusion-Map-Directed Molecular Dynamics

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    Author
    Zheng, Wenwei; Rohrdanz, Mary A.; Clementi, Cecilia
    Date
    2013
    Abstract
    The gap between the time scale of interesting behavior in macromolecular systems and that which our computational resources can afford often limits molecular dynamics (MD) from understanding experimental results and predicting what is inaccessible in experiments. In this paper, we introduce a new sampling scheme, named diffusion-map-directed MD (DM-d-MD), to rapidly explore molecular configuration space. The method uses a diffusion map to guide MD on the fly. DM-d-MD can be combined with other methods to reconstruct the equilibrium free energy, and here, we used umbrella sampling as an example. We present results from two systems: alanine dipeptide and alanine-12. In both systems, we gain tremendous speedup with respect to standard MD both in exploring the configuration space and reconstructing the equilibrium distribution. In particular, we obtain 3 orders of magnitude of speedup over standard MD in the exploration of the configurational space of alanine-12 at 300 K with DM-d-MD. The method is reaction coordinate free and minimally dependent on a priori knowledge of the system. We expect wide applications of DM-d-MD to other macromolecular systems in which equilibrium sampling is not affordable by standard MD.
    Citation
    Zheng, Wenwei, Rohrdanz, Mary A. and Clementi, Cecilia. "Rapid Exploration of Configuration Space with Diffusion-Map-Directed Molecular Dynamics." The Journal of Physical Chemistry C, 117, no. 42 (2013) American Chemical Society: 12769-12776. http://dx.doi.org/10.1021/jp401911h.
    Published Version
    http://dx.doi.org/10.1021/jp401911h
    Keyword
    diffusion map; molecular dynamics; umbrella sampling
    Type
    Journal article
    Publisher
    American Chemical Society
    Citable link to this page
    https://hdl.handle.net/1911/78749
    Rights
    This is an author's peer-reviewed final manuscript, as accepted by the publisher. The published article is copyrighted by the American Chemical Society.
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    • Chemistry Publications [636]
    • Faculty Publications [4990]

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    Home | FAQ | Contact Us | Privacy Notice | Accessibility Statement
    Managed by the Digital Scholarship Services at Fondren Library, Rice University
    Physical Address: 6100 Main Street, Houston, Texas 77005
    Mailing Address: MS-44, P.O.BOX 1892, Houston, Texas 77251-1892
    Site Map