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Multiscale Molecular Modeling

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Book cover Biomolecular Simulations

Part of the book series: Methods in Molecular Biology ((MIMB,volume 924))

Abstract

We review the basic theoretical principles of the adaptive resolution simulation scheme (AdResS). This method allows to change molecular resolution on-the-fly during a simulation by changing the number of degrees of freedom in specific regions of space where the required resolution is higher than in the rest of the system. We also report about recent extensions of the method to the continuum and quantum regimes.

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Notes

  1. 1.

    As defined by Eqs. 3 and 4, μkin(0)≠μ A kin. In fact, \({\mu }_{A}^{{kin}} = {\mu }^{{kin}}(0) + \phi {(0)}^{{kin}} = {\mu }_{B}^{{kin}}\). μkin(w) represents only the contribution of the switched-on DOFs to the kinetic part of chemical potential. The rest is included in φ(w)kin.

  2. 2.

    This is the value that one obtains by using the insertion methods in a hybrid system exclusively composed of hybrid molecules with a fixed level of resolution \(0 \leq w = w(x) = \mathrm{const}. \leq 1\) corresponding to a fixed bulk value μ w(x).

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Acknowledgements

Over the years we have collaborated with many colleagues and students on the topics described in this chapter. Out of them we would like to especially thank K. Kremer, R. Delgado-Buscalioni, C. Junghans, A. B. Poma, S. Poblete, C. Clementi, B. Lambeth, and S. Matysiak for fruitful collaboration and many discussions.

Author information

Authors and Affiliations

  1. National Institute of Chemistry, Ljubljana, Slovenia

    Matej Praprotnik

  2. Department of Mathematics and Computer Science, Freie Universitäat Berlin, Berlin, Germany

    Luigi Delle Site

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  1. Matej Praprotnik
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  2. Luigi Delle Site
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Correspondence to Luigi Delle Site .

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Editors and Affiliations

  1. DSIMB, UMR-S 665, INSERM, rue Alexandre Cabanel 6, Paris, 75015, France

    Luca Monticelli

  2. , Department of Applied Physics, Aalto University, Otakaari, AALTO, FI-00076, Finland

    Emppu Salonen

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Praprotnik, M., Site, L.D. (2013). Multiscale Molecular Modeling. In: Monticelli, L., Salonen, E. (eds) Biomolecular Simulations. Methods in Molecular Biology, vol 924. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-017-5_21

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  • DOI: https://doi.org/10.1007/978-1-62703-017-5_21

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  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-62703-016-8

  • Online ISBN: 978-1-62703-017-5

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