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.
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