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Equilibrium Statistical Mechanics, Non-Hamiltonian Molecular Dynamics, and Novel Applications from Resonance-Free Timesteps to Adiabatic Free Energy Dynamics

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Computer Simulations in Condensed Matter Systems: From Materials to Chemical Biology Volume 1

Part of the book series: Lecture Notes in Physics ((LNP,volume 703))

Abstract

Levinthal’s paradox [1,2], first introduced in the 1960’s (early in the childhood of simulations in Chemistry), serves as a good illustration of the limitations we still face in the application of molecular dynamics (MD). Levinthal reasoned that if we were to assume that every residue in a polypeptide has a least two stable conformations, then a small 100 residue polypeptide would have 2100 possible states. If we were to study such a protein using traditional, state of the art, MD techniques, the native state would only be deduced after a little more than a billion years.

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Author information

Authors and Affiliations

  1. Dept. of Chemistry, New York University, 10003, New York, NY, USA

    J.B. Abrams & M.E. Tuckerman

  2. Courant Institute of Mathematical Sciences, New York University, 10003, New York, NY, USA

    M.E. Tuckerman

  3. T.J. Watson Research Center, International Business Corporation, 218, 10598, Yorktown Heights, NY, USA

    G.J. Martyna

Authors
  1. J.B. Abrams
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  2. M.E. Tuckerman
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  3. G.J. Martyna
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Editor information

Editors and Affiliations

  1. Dipartimento di Fisica, Università di Modena e Reggio Emilia, Via Campi, 213/A, 41100, Modena, Italy

    Mauro Ferrario Professor

  2. Dipartimento di Fisica, INFN, Università di Roma La Sapienza, Piazzale Aldo Moro 2, 00185, Roma, Italy

    Giovanni Ciccotti Professor

  3. Institut für Physik, Universität Mainz, Staudinger Weg 7, 55128, Mainz, Germany

    Kurt Binder Professor

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Abrams, J., Tuckerman, M., Martyna, G. (2006). Equilibrium Statistical Mechanics, Non-Hamiltonian Molecular Dynamics, and Novel Applications from Resonance-Free Timesteps to Adiabatic Free Energy Dynamics. In: Ferrario, M., Ciccotti, G., Binder, K. (eds) Computer Simulations in Condensed Matter Systems: From Materials to Chemical Biology Volume 1. Lecture Notes in Physics, vol 703. Springer, Berlin, Heidelberg. https://doi.org/10.1007/3-540-35273-2_5

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