From the Cover: Simplifying the representation of complex free-energy landscapes using sketch-map.

ABSTRACT: A new scheme, sketch-map, for obtaining a low-dimensional representation of the region of phase space explored during an enhanced dynamics simulation is proposed. We show evidence, from an examination of the distribution of pairwise distances between frames, that some features of the free-energy surface are inherently high-dimensional. This makes dimensionality reduction problematic because the data does not satisfy the assumptions made in conventional manifold learning algorithms We therefore propose that when dimensionality reduction is performed on trajectory data one should think of the resultant embedding as a quickly sketched set of directions rather than a road map. In other words, the embedding tells one about the connectivity between states but does not provide the vectors that co

SUBMITTER: Ceriotti M 

PROVIDER: S-EPMC3156203 | biostudies-literature | 2011 Aug

REPOSITORIES: biostudies-literature