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Relative Entropy and Optimization-Driven Coarse-Graining Methods in VOTCA

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  • S Y Mashayak
  • Mara N Jochum
  • Konstantin Koschke
  • N R Aluru
  • Victor Rühle
  • Christoph Junghans

Abstract

We discuss recent advances of the VOTCA package for systematic coarse-graining. Two methods have been implemented, namely the downhill simplex optimization and the relative entropy minimization. We illustrate the new methods by coarse-graining SPC/E bulk water and more complex water-methanol mixture systems. The CG potentials obtained from both methods are then evaluated by comparing the pair distributions from the coarse-grained to the reference atomistic simulations. In addition to the newly implemented methods, we have also added a parallel analysis framework to improve the computational efficiency of the coarse-graining process.

Suggested Citation

  • S Y Mashayak & Mara N Jochum & Konstantin Koschke & N R Aluru & Victor Rühle & Christoph Junghans, 2015. "Relative Entropy and Optimization-Driven Coarse-Graining Methods in VOTCA," PLOS ONE, Public Library of Science, vol. 10(7), pages 1-20, July.
    • Handle: RePEc:plo:pone00:0131754
    DOI: 10.1371/journal.pone.0131754
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