Markov State Models and Molecular Alchemy

  • In recent years Markov State Models (MSMs) have attracted a consid- erable amount of attention with regard to modelling conformation changes and associated function of biomolecular systems. They have been used successfully, e.g., for peptides including time-resolved spectroscopic experiments, protein function and protein folding , DNA and RNA, and ligand-receptor interaction in drug design and more complicated multivalent scenarios. In this article a novel reweighting scheme is introduced that allows to construct an MSM for certain molecular system out of an MSM for a similar system. This permits studying how molecular properties on long timescales differ between similar molecular systems without performing full molecular dynamics simulations for each system under con- sideration. The performance of the reweighting scheme is illustrated for simple test cases including one where the main wells of the respective energy landscapes are located differently and an alchemical transformation of butane to pentane where the dimension of the state space is changed.

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Author:Christof Schütte, Adam Nielsen, Marcus Weber
Document Type:Article
Parent Title (English):Molecular Physics
Volume:113
Issue:1
First Page:69
Last Page:78
Tag:Girsanov ; Reweighting
MSM
Year of first publication:2015
Preprint:urn:nbn:de:0297-zib-46718
DOI:http://dx.doi.org/10.1080/00268976.2014.944597

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