A meshless discretization method for Markov state models applied to explicit water peptide folding simulations. (English) Zbl 1269.82072
Griebel, Michael (ed.) et al., Meshfree methods for partial differential equations VI. Selected papers of the sixth international workshop, Bonn, Germany, October 4–6, 2011. Berlin: Springer (ISBN 978-3-642-32978-4/hbk; 978-3-642-32979-1/ebook). Lecture Notes in Computational Science and Engineering 89, 141-154 (2013).
Summary: 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 tri-alanine, we are able to compute the same distribution of a long term simulation in less computing time.
For the entire collection see [Zbl 1257.65003].
For the entire collection see [Zbl 1257.65003].
MSC:
| 82D60 | Statistical mechanics of polymers |
| 82-08 | Computational methods (statistical mechanics) (MSC2010) |
| 60J75 | Jump processes (MSC2010) |
Keywords:
molecular dynamics; conformation dynamics; robust Perron cluster analysis; Markovianity; transfer operator; partition of unityReferences:
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