TY - GEN A1 - Fackeldey, Konstantin A1 - Bujotzek, Alexander A1 - Weber, Marcus T1 - A Meshless Discretization Method for Markov State Models Applied to Explicit Water Peptide Folding Simulations N2 - 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. KW - Markov State Models Y1 - 2015 UR - https://opus4.kobv.de/opus4-matheon/frontdoor/index/index/docId/1302 UR - https://nbn-resolving.org/urn:nbn:de:0296-matheon-13020 ER -