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International Journal for Multiscale Computational Engineering
IF: 1.016 5-Year IF: 1.194 SJR: 0.554 SNIP: 0.68 CiteScore™: 1.18

ISSN Print: 1543-1649
ISSN Online: 1940-4352

International Journal for Multiscale Computational Engineering

DOI: 10.1615/IntJMultCompEng.v4.i5-6.120
pages 791-802

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

Aiqin Li
Scientific Computational Research Center, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
Haim Waisman
Department of Civil Engineering and Engineering Mechanics, Columbia University, New York, New York 10027, USA
Jacob Fish
Civil Engineering and Engineering Mechanics, Columbia University, New York, New York 10027, USA

ABSTRACT

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 α-D-glucopyranose monomers.