2010/03/04 by Hiroshi Fujisaki, Motoyuki Shiga, Akinori Kidera · 1 citation
Physics and Astronomy · #physics.bio-ph #physics.comp-ph
paper · pdf · doi:10.1063/1.3372802
20 pages, 5 figures, submitted to J. Chem. Phys
arxiv created 2010/03/04 · arxiv updated 2015/05/18
For sampling multiple pathways in a rugged energy landscape, we propose a novel action-based path sampling method using the Onsager-Machlup action functional. Inspired by the Fourier-path integral simulation of a quantum mechanical system, a path in Cartesian space is transformed into that in Fourier space, and an overdamped Langevin equation is derived for the Fourier components to achieve a canonical ensemble of the path at a finite temperature. To avoid "path trapping" around an initially guessed path, the path sampling method is further combined with a powerful sampling technique, the replica exchange method. The principle and algorithm of our method is numerically demonstrated for a model two-dimensional system with a bifurcated potential landscape. The results are compared with those of conventional transition path sampling and the equilibrium theory, and the error due to path discretization is also discussed.