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A Meshless Discretization Method for Markov State Models Applied to Explicit Water Peptide Folding Simulations

  • Konstantin Fackeldey
  • Alexander Bujotzek
  • Marcus Weber
Conference paper
Part of the Lecture Notes in Computational Science and Engineering book series (LNCSE, volume 89)

Abstract

Markov State Models (MSMs) are widely used to represent molecular conformational changes as jump-like transitions between subsets of the conformational state space. However, the simulation of peptide folding in explicit water is usually said to be unsuitable for the MSM framework. In this article, we summarize the theoretical background of MSMs and indicate that explicit water simulations do not contradict these principles. The algorithmic framework of a meshless conformational space discretization is applied to an explicit water system and the sampling results are compared to a long-term molecular dynamics trajectory. The meshless discretization approach is based on spectral clustering of stochastic matrices (MSMs) and allows for a parallelization of MD simulations. In our example of Trialanine we were able to compute the same distribution of a long term simulation in less computing time.

Keywords

Molecular dynamics Conformation dynamics Robust perron cluster analysis Markovianity Transfer operator Partition of unity 

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Copyright information

© Springer-Verlag Berlin Heidelberg 2013

Authors and Affiliations

  • Konstantin Fackeldey
    • 1
  • Alexander Bujotzek
    • 1
  • Marcus Weber
    • 1
  1. 1.Zuse Institute Berlin (ZIB)BerlinGermany

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