Abstract

A theory to realize a multiscale dynamics of protein is proposed based on the generalized Langevin equation combined with the 3D-RISM theory. The idea of normal mode analysis (NMA) is adopted to decouple the dynamics into different modes having respective time scales. In order to decouple the modes, the variance–covariance matrix concerning the structural fluctuation of protein in solution is diagonalized, instead of the Hessian matrix of a harmonic oscillator in vacuum. An algorithm to estimate the friction coefficient exerted on each atom of protein due to solvent is also proposed.

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