Simplifying the representation of complex free-energy landscapes using sketch-map
نویسندگان
چکیده
منابع مشابه
From the Cover: Simplifying the representation of complex free-energy landscapes using sketch-map.
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...
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with Vt the volume of the space visited in the simulation and D the dimension. Ω is the solid angle in D-dimensional spherical coordinates and w(r,Ω, t) the weight of the node at position (r,Ω), at time t. For simplicity spherical symmetry of the energy landscape (U(x) = U(r)) will be assumed. For large enough t, w(r, t) is proportional to the stationary solution. Taking U(r) in the units of kB...
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ژورنال
عنوان ژورنال: Proceedings of the National Academy of Sciences
سال: 2011
ISSN: 0027-8424,1091-6490
DOI: 10.1073/pnas.1108486108