BOCS: Bottom-up Open-source Coarse-graining Software

Nicholas J.H. Dunn, Kathryn M. Lebold, Michael R. Delyser, Joseph F. Rudzinski, W. G. Noid

Research output: Contribution to journalArticle

14 Scopus citations

Abstract

We present the BOCS toolkit as a suite of open source software tools for parametrizing bottom-up coarse-grained (CG) models to accurately reproduce structural and thermodynamic properties of high-resolution models. The BOCS toolkit complements available software packages by providing robust implementations of both the multiscale coarse-graining (MS-CG) force-matching method and also the generalized-Yvon-Born-Green (g-YBG) method. The g-YBG method allows one to analyze and to calculate MS-CG potentials in terms of structural correlations. Additionally, the BOCS toolkit implements an extended ensemble framework for optimizing the transferability of bottom-up potentials, as well as a self-consistent pressure-matching method for accurately modeling the pressure equation of state for homogeneous systems. We illustrate these capabilities by parametrizing transferable potentials for CG models that accurately model the structure, pressure, and compressibility of liquid alkane systems and by quantifying the role of many-body correlations in determining the calculated pair potential for a one-site CG model of liquid methanol.

Original languageEnglish (US)
Pages (from-to)3363-3377
Number of pages15
JournalJournal of Physical Chemistry B
Volume122
Issue number13
DOIs
StatePublished - Apr 5 2018

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    Dunn, N. J. H., Lebold, K. M., Delyser, M. R., Rudzinski, J. F., & Noid, W. G. (2018). BOCS: Bottom-up Open-source Coarse-graining Software. Journal of Physical Chemistry B, 122(13), 3363-3377. https://doi.org/10.1021/acs.jpcb.7b09993