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Order parameters for macromolecules: Application to multiscale simulation
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DOI：10.1063/1.3524532.png)
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Order parameters (OPs) characterizing the nanoscale features of macromolecules are presented. They are generated in a general fashion so that they do not need to be redesigned with each new application. They evolve on time scales much longer than 10(-14) s typical for individual atomic collisions/vibrations. The list of OPs can be automatically increased, and completeness can be determined via a correlation analysis. They serve as the basis of a multiscale analysis that starts with the N-atom Liouville equation and yields rigorous Smoluchowski/Langevin equations of stochastic OP dynamics. Such OPs and the multiscale analysis imply computational algorithms that we demonstrate in an application to ribonucleic acid structural dynamics for 50 ns. (C) 2011 American Institute of Physics. [doi:10.1063/1.3524532]
Keyword:
MOLECULAR-DYNAMICS SIMULATIONS
NORMAL-MODE ANALYSIS
FREE-ENERGY
ALL-ATOM
RNA HAIRPINS
EXTRAPOLATION
LANDSCAPE
SPACE
ANGLE
PATH
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IF:
3.1
论文数:
7.2W
被引数:
23.2W
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