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International Journal for Multiscale Computational Engineering
Импакт фактор: 1.016 5-летний Импакт фактор: 1.194 SJR: 0.554 SNIP: 0.68 CiteScore™: 1.18

ISSN Печать: 1543-1649
ISSN Онлайн: 1940-4352

Выпуски:
Том 17, 2019 Том 16, 2018 Том 15, 2017 Том 14, 2016 Том 13, 2015 Том 12, 2014 Том 11, 2013 Том 10, 2012 Том 9, 2011 Том 8, 2010 Том 7, 2009 Том 6, 2008 Том 5, 2007 Том 4, 2006 Том 3, 2005 Том 2, 2004 Том 1, 2003

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

Краткое описание

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.


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