Journal
PHYSICAL REVIEW E
Volume 62, Issue 6, Pages 8438-8448Publisher
AMER PHYSICAL SOC
DOI: 10.1103/PhysRevE.62.8438
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Principal component analysis, also called essential dynamics, is a powerful tool for finding global, correlated motions in atomic simulations of macromolecules. It has become an established technique for analyzing molecular dynamics simulations of proteins. The first few principal components of simulations of large proteins often resemble cosines. We derive the principal components for high-dimensional random diffusion, which are almost perfect cosines. This resemblance between protein simulations and noise implies that for many proteins the time scales of current simulations are too short to obtain convergence of collective motions.
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