Journal
JOURNAL OF CHEMICAL PHYSICS
Volume 134, Issue 12, Pages -Publisher
AMER INST PHYSICS
DOI: 10.1063/1.3569857
Keywords
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Funding
- National Science Foundation (NSF) [0835824, 0835712]
- NSF [CHE-0349303, DMS-0650413, CNS-0421109, CNS-0821727, EIA-0216467]
- Welch Foundation [C-1570]
- Sloan Foundation
- Direct For Mathematical & Physical Scien
- Division Of Chemistry [0835824, 0835712] Funding Source: National Science Foundation
- Division Of Mathematical Sciences
- Direct For Mathematical & Physical Scien [0847388] Funding Source: National Science Foundation
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We present a multiscale method for the determination of collective reaction coordinates for macromolecular dynamics based on two recently developed mathematical techniques: diffusion map and the determination of local intrinsic dimensionality of large datasets. Our method accounts for the local variation of molecular configuration space, and the resulting global coordinates are correlated with the time scales of the molecular motion. To illustrate the approach, we present results for two model systems: all-atom alanine dipeptide and coarse-grained src homology 3 protein domain. We provide clear physical interpretation for the emerging coordinates and use them to calculate transition rates. The technique is general enough to be applied to any system for which a Boltzmann-sampled set of molecular configurations is available. (C) 2011 American Institute of Physics. [doi:10.1063/1.3569857]
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