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

Nicholas J H Dunn1, Kathryn M Lebold1, Michael R DeLyser1

  • 1Department of Chemistry , The Pennsylvania State University , University Park , Pennsylvania 16802 , United States.

The Journal of Physical Chemistry. B
|December 12, 2017
PubMed
Summary
This summary is machine-generated.

The BOCS toolkit offers open-source software for creating accurate bottom-up coarse-grained (CG) models. It enhances CG model development by implementing advanced force-matching and analysis methods for improved structural and thermodynamic property reproduction.

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Area of Science:

  • Computational chemistry and materials science.
  • Development of molecular modeling software.
  • Coarse-grained (CG) modeling techniques.

Background:

  • Accurate parametrization of bottom-up coarse-grained (CG) models is crucial for simulating large systems.
  • Existing software packages may lack comprehensive methods for CG potential development.
  • Reproducing structural and thermodynamic properties requires robust computational tools.

Purpose of the Study:

  • Introduce the BOCS toolkit, a new suite of open-source software tools.
  • Provide robust implementations of multiscale coarse-graining (MS-CG) force-matching and generalized-Yvon-Born-Green (g-YBG) methods.
  • Enhance the development and transferability of bottom-up CG models.

Main Methods:

  • Implementation of the multiscale coarse-graining (MS-CG) force-matching method.
  • Utilization of the generalized-Yvon-Born-Green (g-YBG) method for analyzing structural correlations.
  • Application of an extended ensemble framework for optimizing potential transferability.
  • Employing a self-consistent pressure-matching method for equation of state calculations.

Main Results:

  • Parametrization of transferable potentials for CG models of liquid alkanes, accurately reproducing structure, pressure, and compressibility.
  • Quantification of many-body correlation effects on pair potentials for a CG model of liquid methanol.
  • Demonstration of BOCS toolkit's capability in developing accurate and transferable CG potentials.

Conclusions:

  • The BOCS toolkit provides essential tools for accurate bottom-up CG model parametrization.
  • The implemented methods enable robust analysis and optimization of CG potentials.
  • BOCS facilitates the accurate modeling of structural and thermodynamic properties in molecular simulations.