Efficient, Regularized, and Scalable Algorithms for Multiscale Coarse-Graining

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• 作者：Lanyuan Lu ; Sergei Izvekov ; Avisek Das ; Hans C. Andersen ; Gregory A. Voth
• 刊名：Journal of Chemical Theory and Computation
• 出版年：2010
• 出版时间：March 9, 2010
• 年：2010
• 卷：6
• 期：3
• 页码：954-965
• 全文大小：208K
• 年卷期：v.6,no.3(March 9, 2010)
• ISSN：1549-9626

文摘

The multiscale coarse-graining (MS-CG) method obtains CG interactions from atomistic configurations, as demonstrated previously for a variety of soft matter and biological systems. In this article, recent advances in MS-CG algorithms are described, and a recently developed computer program MSCGFM for MS-CG calculations is introduced. The algorithms enhance the efficiency and stability of MS-CG computations, and these algorithms are incorporated into the MSCGFM program. As a result of these efforts, MS-CG calculations on large scale systems such as peptide and proteins can become tractable, and the numerical stability of solutions for ill-posed MS-CG problems can be regularized efficiently. Various parallelization strategies are also discussed.