title: Efficient, Regularized, and Scalable Algorithms for Multiscale Coarse-Graining.
abstract: 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.
authors.affiliation: Center for Biophysical Modeling and Simulation and Department of Chemistry, University of Utah, Salt Lake City, Utah 84112-0850, and Department of Chemistry, Stanford University, Stanford, California 94305.
authors.forename: Lanyuan
authors.initials: L
authors.lastname: Lu
authors.affiliation: Center for Biophysical Modeling and Simulation and Department of Chemistry, University of Utah, Salt Lake City, Utah 84112-0850, and Department of Chemistry, Stanford University, Stanford, California 94305.
authors.forename: Sergei
authors.initials: S
authors.lastname: Izvekov
authors.affiliation: Center for Biophysical Modeling and Simulation and Department of Chemistry, University of Utah, Salt Lake City, Utah 84112-0850, and Department of Chemistry, Stanford University, Stanford, California 94305.
authors.forename: Avisek
authors.initials: A
authors.lastname: Das
authors.affiliation: Center for Biophysical Modeling and Simulation and Department of Chemistry, University of Utah, Salt Lake City, Utah 84112-0850, and Department of Chemistry, Stanford University, Stanford, California 94305.
authors.forename: Hans C
authors.initials: HC
authors.lastname: Andersen
authors.affiliation: Center for Biophysical Modeling and Simulation and Department of Chemistry, University of Utah, Salt Lake City, Utah 84112-0850, and Department of Chemistry, Stanford University, Stanford, California 94305.
authors.forename: Gregory A
authors.initials: GA
authors.lastname: Voth