Fast equilibration of coarse-grained polymeric liquids

Ozog, David; McCarty, Jay; Gossett, Grant; Malony, Allen D.; Guenza, Marina

doi:10.1016/j.jocs.2015.04.015

Fast equilibration of coarse-grained polymeric liquids

Journal Article · 20 April 2015 · Journal of Computational Science

DOI:https://doi.org/10.1016/j.jocs.2015.04.015· OSTI ID:1418536

Ozog, David ^[1]; McCarty, Jay ^[2]; Gossett, Grant ^[2]; Malony, Allen D. ^[2]; Guenza, Marina ^[2]

Univ. of Oregon, Eugene, OR (United States); DOE Office of Scientific and Technical Information (OSTI)
Univ. of Oregon, Eugene, OR (United States)

The study of macromolecular systems may require large computer simulations that are too time consuming and resource intensive to execute in full atomic detail. The integral equation coarse-graining approach by Guenza and co-workers enables the exploration of longer time and spatial scales without sacrificing thermodynamic consistency, by approximating collections of atoms using analytically-derived soft-sphere potentials. Because coarse-grained (CG) characterizations evolve polymer systems far more efficiently than the corresponding united atom (UA) descriptions, we can feasibly equilibrate a CG system to a reasonable geometry, then transform back to the UA description for a more complete equilibration. Automating the transformation between the two different representations simultaneously exploits CG efficiency and UA accuracy. By iteratively mapping back and forth between CG and UA, we can quickly guide the simulation towards a configuration that would have taken many more time steps within the UA representation alone. Accomplishing this feat requires a diligent workflow for managing input/output coordinate data between the different steps, deriving the potential at runtime, and inspecting convergence. Here in this article, we present a lightweight workflow environment that accomplishes such fast equilibration without user intervention. The workflow supports automated mapping between the CG and UA descriptions in an iterative, scalable, and customizable manner. We describe this technique, examine its feasibility, and analyze its correctness.

Research Organization:: Krell Inst., Ames, IA (United States)

Sponsoring Organization:: National Science Foundation; USDOE

Grant/Contract Number:: FG02-97ER25308; FG02-07ER25826; SC0001777

OSTI ID:: 1418536

Alternate ID(s):: OSTI ID: 1251655

Journal Information:: Journal of Computational Science, Journal Name: Journal of Computational Science Journal Issue: C Vol. 9; ISSN 1877-7503

Publisher:: ElsevierCopyright Statement

Country of Publication:: United States

Language:: English

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Cited By (1)

Hierarchical modeling of polystyrene melts: From soft blobs to atomistic resolution Zhang, Guojie; Chazirakis, Anthony; Harmandaris, Vagelis A. arXiv https://doi.org/10.48550/arxiv.1808.03205	preprint	January 2018

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37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY
LAMMPS
atomistic simulation
coarse-graining
polymeric liquids
scientific workflows

Fast equilibration of coarse-grained polymeric liquids

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