Multi-scale dynamics simulation of protein based on the generalized Langevin equation combined with 3D-RISM theory

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.