Metadynamics in the conformational space non-linearly dimensionally reduced by Isomap

Result code in IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F60461373%3A22330%2F11%3A43891977" target="_blank" >RIV/60461373:22330/11:43891977 - isvavai.cz</a>
Result on the web
<a href="http://dx.doi.org/10.1063/1.3660208" target="_blank" >http://dx.doi.org/10.1063/1.3660208</a>
DOI - Digital Object Identifier
<a href="http://dx.doi.org/10.1063/1.3660208" target="_blank" >10.1063/1.3660208</a>

Result language
angličtina
Original language name
Metadynamics in the conformational space non-linearly dimensionally reduced by Isomap
Original language description
Atomic motions in molecules are not linear. This infers that nonlinear dimensionality reduction methods can outperform linear ones in analysis of collective atomic motions. In addition, nonlinear collective motions can be used as potentially efficient guides for biased simulation techniques. Here we present a simulation with a bias potential acting in the directions of collective motions determined by a nonlinear dimensionality reduction method. Ad hoc generated conformations of trans,trans-1,2,4-trifluorocyclooctane were analyzed by Isomap method to map these 72-dimensional coordinates to three dimensions, as described by Brown and co-workers [J. Chem. Phys. 129, 064118 (2008)]. Metadynamics employing the three-dimensional embeddings as collective variables was applied to explore all relevant conformations of the studied system and to calculate its conformational free energy surface. The method sampled all relevant conformations (boat, boat-chair, and crown) and corresponding transiti
Czech name
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Czech description
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Type
J<sub>x</sub> - Unclassified - Peer-reviewed scientific article (Jimp, Jsc and Jost)
CEP classification
CE - Biochemistry
OECD FORD branch
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Publication year
2011
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

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