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

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

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...

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Main Authors: S Y Mashayak, Mara N Jochum, Konstantin Koschke, N R Aluru, Victor Rühle, Christoph Junghans
Format: Article
Language:English
Published: Public Library of Science (PLoS) 2015-01-01
Series:PLoS ONE
Online Access:http://europepmc.org/articles/PMC4507862?pdf=render
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spelling doaj-1aac32f23d904f058f59ce68c0e1cce92020-11-25T02:14:07ZengPublic Library of Science (PLoS)PLoS ONE1932-62032015-01-01107e013175410.1371/journal.pone.0131754Relative Entropy and Optimization-Driven Coarse-Graining Methods in VOTCA.S Y MashayakMara N JochumKonstantin KoschkeN R AluruVictor RühleChristoph JunghansWe 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.http://europepmc.org/articles/PMC4507862?pdf=render
collection DOAJ
language English
format Article
sources DOAJ
author S Y Mashayak
Mara N Jochum
Konstantin Koschke
N R Aluru
Victor Rühle
Christoph Junghans
spellingShingle S Y Mashayak
Mara N Jochum
Konstantin Koschke
N R Aluru
Victor Rühle
Christoph Junghans
Relative Entropy and Optimization-Driven Coarse-Graining Methods in VOTCA.
PLoS ONE
author_facet S Y Mashayak
Mara N Jochum
Konstantin Koschke
N R Aluru
Victor Rühle
Christoph Junghans
author_sort S Y Mashayak
title Relative Entropy and Optimization-Driven Coarse-Graining Methods in VOTCA.
title_short Relative Entropy and Optimization-Driven Coarse-Graining Methods in VOTCA.
title_full Relative Entropy and Optimization-Driven Coarse-Graining Methods in VOTCA.
title_fullStr Relative Entropy and Optimization-Driven Coarse-Graining Methods in VOTCA.
title_full_unstemmed Relative Entropy and Optimization-Driven Coarse-Graining Methods in VOTCA.
title_sort relative entropy and optimization-driven coarse-graining methods in votca.
publisher Public Library of Science (PLoS)
series PLoS ONE
issn 1932-6203
publishDate 2015-01-01
description 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.
url http://europepmc.org/articles/PMC4507862?pdf=render
work_keys_str_mv AT symashayak relativeentropyandoptimizationdrivencoarsegrainingmethodsinvotca
AT maranjochum relativeentropyandoptimizationdrivencoarsegrainingmethodsinvotca
AT konstantinkoschke relativeentropyandoptimizationdrivencoarsegrainingmethodsinvotca
AT nraluru relativeentropyandoptimizationdrivencoarsegrainingmethodsinvotca
AT victorruhle relativeentropyandoptimizationdrivencoarsegrainingmethodsinvotca
AT christophjunghans relativeentropyandoptimizationdrivencoarsegrainingmethodsinvotca
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