A Space-Time Multiscale Method for Molecular Dynamics Simulations of Biomolecules

A novel multiscale approach for molecular-dynamics simulations is developed. The goal of this method is to reduce the time cost of molecular-dynamics simulations without loss of accuracy in the quantities of interest. The proposed approach consists of the waveform relaxation scheme aimed at capturing the high-frequency motions and a coarse-scale solution in space and time aimed at resolving smooth features (in both space and time domains) of the system. The use of proper orthogonal decomposition (POD) modes at the coarse-grained level has been found to accelerate convergence of the waveform relaxation scheme. The accuracy and efficiency of this method are reported by applying it to a model problem of chain of fi-D-glucopyranose monomers.

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