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

  • J.B. Abrams
  • M.E. Tuckerman
  • G.J. Martyna
Chapter
Part of the Lecture Notes in Physics book series (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.

Keywords

Phase Space Partition Function Canonical Ensemble Multiple Time Scale Phase Space Volume 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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Copyright information

© Springer 2006

Authors and Affiliations

  • J.B. Abrams
    • 1
  • M.E. Tuckerman
    • 1
    • 2
  • G.J. Martyna
    • 3
  1. 1.Dept. of ChemistryNew York UniversityNew YorkUSA
  2. 2.Courant Institute of Mathematical SciencesNew York UniversityNew YorkUSA
  3. 3.T.J. Watson Research CenterInternational Business CorporationYorktown HeightsUSA

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