A Meshless Discretization Method for Markov State Models Applied to Explicit Water Peptide Folding Simulations
Please always quote using this URN:urn:nbn:de:0296-matheon-13020
- 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.
Author: | Konstantin Fackeldey, Alexander Bujotzek, Marcus Weber |
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URN: | urn:nbn:de:0296-matheon-13020 |
Referee: | Volker Mehrmann |
Document Type: | Preprint, Research Center Matheon |
Language: | English |
Date of first Publication: | 2015/12/23 |
Release Date: | 2015/12/23 |
Tag: | Markov State Models |
Institute: | Zuse Institute Berlin (ZIB) |
MSC-Classification: | 65-XX NUMERICAL ANALYSIS / 65Cxx Probabilistic methods, simulation and stochastic differential equations (For theoretical aspects, see 68U20 and 60H35) / 65C05 Monte Carlo methods |
Preprint Number: | 1091 |