Combining Metadynamics and Integrated Tempering Sampling
نویسندگان
چکیده
منابع مشابه
Sampling free energy surfaces as slices by combining umbrella sampling and metadynamics
Metadynamics (MTD) is a very powerful technique to sample high-dimensional free energy landscapes, and due to its self-guiding property, the method has been successful in studying complex reactions and conformational changes. MTD sampling is based on filling the free energy basins by biasing potentials and thus for cases with flat, broad, and unbound free energy wells, the computational time to...
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iii ACKNOWLEDGEMENTS I would like to thank my advisors Dana Randall and Eric Vigoda for their guidance and support, which they gave generously. I was fortunate to have the opportunity to work with two of the leading researchers in my field. Dana never ceased to surprise me with her quick insights and ability to get to crux of a problem. I thoroughly enjoyed working with Eric and am always inspi...
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Multimodal structures in the sampling density (e.g. two competing phases) can be a serious problem for traditional Markov Chain Monte Carlo (MCMC), because correct sampling of the different structures can only be guaranteed for infinite sampling time. Samples may not decouple from the initial configuration for a long time and autocorrelation times may be hard to determine. We analyze a suitable...
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The free-energy landscape of the alpha-helix of protein G is studied by means of metadynamics coupled with a solute tempering algorithm. Metadynamics allows to overcome large energy barriers, whereas solute tempering improves the sampling with an affordable computational effort. From the sampled free-energy surface we are able to reproduce a number of experimental observations, such as the fact...
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Accurate and precise structural ensembles of proteins and macromolecular complexes can be obtained with metainference, a recently proposed Bayesian inference method that integrates experimental information with prior knowledge and deals with all sources of errors in the data as well as with sample heterogeneity. The study of complex macromolecular systems, however, requires an extensive conform...
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ژورنال
عنوان ژورنال: The Journal of Physical Chemistry Letters
سال: 2018
ISSN: 1948-7185
DOI: 10.1021/acs.jpclett.8b03005