Relative entropy and optimization-driven coarse-graining methods in VOTCA

Mashayak, S. Y.; Jochum, Mara N.; Koschke, Konstantin; Aluru, N. R.; Rühle, Victor; Junghans, Christoph; Huang, Xuhui

doi:10.1371/journal.pone.0131754

Title: Relative entropy and optimization-driven coarse-graining methods in VOTCA

Journal Article · Mon Jul 20 00:00:00 EDT 2015 · PLoS ONE

DOI:https://doi.org/10.1371/journal.pone.0131754· OSTI ID:1221673

Mashayak, S. Y. ^[1]; Jochum, Mara N. ^[2]; Koschke, Konstantin ^[2]; Aluru, N. R. ^[1]; Rühle, Victor ^[3]; Junghans, Christoph ^[4]; Huang, Xuhui ^[5]

Univ. of Illinois at Urbana-Champaign, Urbana, IL (United States)
Max Planck Institute for Polymer Research, Mainz (Germany)
Univ. of Cambridge, Cambridge (United Kingdom)
Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
Hong Kong Univ., Hong Kong (China)

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.We have also added a parallel analysis framework to improve the computational efficiency of the coarse-graining process.

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Research Organization:: Los Alamos National Laboratory (LANL), Los Alamos, NM (United States)

Sponsoring Organization:: USDOE

Grant/Contract Number:: AC52-06NA25396

OSTI ID:: 1221673

Report Number(s):: LA-UR-13-26878; TRN: US1600373

Journal Information:: PLoS ONE, Vol. 10, Issue 7; ISSN 1932-6203

Publisher:: Public Library of ScienceCopyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 53 works

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Title: Relative entropy and optimization-driven coarse-graining methods in VOTCA

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