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

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

Authors:
 [1];  [2];  [2];  [1];  [3];  [4];  [5]
+ Show Author Affiliations
  1. Univ. of Illinois at Urbana-Champaign, Urbana, IL (United States)
  2. Max Planck Institute for Polymer Research, Mainz (Germany)
  3. Univ. of Cambridge, Cambridge (United Kingdom)
  4. Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
  5. Hong Kong Univ., Hong Kong (China)
Publication Date:
Research Org.:
Los Alamos National Laboratory (LANL), Los Alamos, NM (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
1221673
Report Number(s):
LA-UR-13-26878
Journal ID: ISSN 1932-6203; TRN: US1600373
Grant/Contract Number:  
AC52-06NA25396
Resource Type:
Accepted Manuscript
Journal Name:
PLoS ONE
Additional Journal Information:
Journal Volume: 10; Journal Issue: 7; Journal ID: ISSN 1932-6203
Publisher:
Public Library of Science
Country of Publication:
United States
Language:
English
Subject:
74 ATOMIC AND MOLECULAR PHYSICS; entropy; algorithms; optimization; simulation and modeling; methanol; thermodynamics; reflection; potential energy

Citation Formats

Mashayak, S. Y., Jochum, Mara N., Koschke, Konstantin, Aluru, N. R., Rühle, Victor, Junghans, Christoph, and Huang, Xuhui. Relative entropy and optimization-driven coarse-graining methods in VOTCA. United States: N. p., 2015. Web. doi:10.1371/journal.pone.0131754.
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Mashayak, S. Y., Jochum, Mara N., Koschke, Konstantin, Aluru, N. R., Rühle, Victor, Junghans, Christoph, & Huang, Xuhui. Relative entropy and optimization-driven coarse-graining methods in VOTCA. United States. https://doi.org/10.1371/journal.pone.0131754
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Mashayak, S. Y., Jochum, Mara N., Koschke, Konstantin, Aluru, N. R., Rühle, Victor, Junghans, Christoph, and Huang, Xuhui. Mon . "Relative entropy and optimization-driven coarse-graining methods in VOTCA". United States. https://doi.org/10.1371/journal.pone.0131754. https://www.osti.gov/servlets/purl/1221673.
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@article{osti_1221673,
title = {Relative entropy and optimization-driven coarse-graining methods in VOTCA},
author = {Mashayak, S. Y. and Jochum, Mara N. and Koschke, Konstantin and Aluru, N. R. and Rühle, Victor and Junghans, Christoph and Huang, Xuhui},
abstractNote = {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.},
doi = {10.1371/journal.pone.0131754},
journal = {PLoS ONE},
number = 7,
volume = 10,
place = {United States},
year = {Mon Jul 20 00:00:00 EDT 2015},
month = {Mon Jul 20 00:00:00 EDT 2015}
}
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https://doi.org/10.1371/journal.pone.0131754
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Multiscale simulation of small peptides: Consistent conformational sampling in atomistic and coarse-grained models
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STOCK: Structure mapper and online coarse-graining kit for molecular simulations
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Hybrid Approaches to Coarse-Graining using the VOTCA Package: Liquid Hexane
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General purpose molecular dynamics simulations fully implemented on graphics processing units
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Kirkwood–Buff Coarse-Grained Force Fields for Aqueous Solutions
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  • Ganguly, Pritam; Mukherji, Debashish; Junghans, Christoph
  • Journal of Chemical Theory and Computation, Vol. 8, Issue 5
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GROMACS 4:  Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation
journal, February 2008

  • Hess, Berk; Kutzner, Carsten; van der Spoel, David
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Optimized intermolecular potential functions for liquid alcohols
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journal, February 2005

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  • DOI: 10.1021/jp044629q

The MARTINI Force Field:  Coarse Grained Model for Biomolecular Simulations
journal, July 2007

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Multiscale simulation of soft matter systems – from the atomistic to the coarse-grained level and back
journal, January 2009

  • Peter, Christine; Kremer, Kurt
  • Soft Matter, Vol. 5, Issue 22
  • DOI: 10.1039/b912027k

Multiscale modeling of soft matter: scaling of dynamics
journal, January 2011

  • Fritz, Dominik; Koschke, Konstantin; Harmandaris, Vagelis A.
  • Physical Chemistry Chemical Physics, Vol. 13, Issue 22
  • DOI: 10.1039/c1cp20247b

Phase-space overlap measures. I. Fail-safe bias detection in free energies calculated by molecular simulation
journal, August 2005

  • Wu, Di; Kofke, David A.
  • The Journal of Chemical Physics, Vol. 123, Issue 5
  • DOI: 10.1063/1.1992483

Representability problems for coarse-grained water potentials
journal, April 2007

  • Johnson, Margaret E.; Head-Gordon, Teresa; Louis, Ard A.
  • The Journal of Chemical Physics, Vol. 126, Issue 14
  • DOI: 10.1063/1.2715953

Extended ensemble approach for deriving transferable coarse-grained potentials
journal, January 2009

  • Mullinax, J. W.; Noid, W. G.
  • The Journal of Chemical Physics, Vol. 131, Issue 10
  • DOI: 10.1063/1.3220627

Coarse-graining errors and numerical optimization using a relative entropy framework
journal, March 2011

  • Chaimovich, Aviel; Shell, M. Scott
  • The Journal of Chemical Physics, Vol. 134, Issue 9
  • DOI: 10.1063/1.3557038

Perspective: Coarse-grained models for biomolecular systems
journal, September 2013

  • Noid, W. G.
  • The Journal of Chemical Physics, Vol. 139, Issue 9
  • DOI: 10.1063/1.4818908

Potential energy functions for atomic-level simulations of water and organic and biomolecular systems
journal, May 2005

  • Jorgensen, W. L.; Tirado-Rives, J.
  • Proceedings of the National Academy of Sciences, Vol. 102, Issue 19
  • DOI: 10.1073/pnas.0408037102

A family of primitive models of water: three-, four and five-site models
journal, February 1997

Coarse-grained molecular models of water: a review
journal, July 2012

A Simplex Method for Function Minimization
journal, January 1965

On the Determination of Molecular Fields. I. From the Variation of the Viscosity of a Gas with Temperature
journal, October 1924

  • Jones, J. E.
  • Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences, Vol. 106, Issue 738
  • DOI: 10.1098/rspa.1924.0081

Comparative atomistic and coarse-grained study of water: What do we lose by coarse-graining?
journal, January 2009

Multiscale Simulation of Soft Matter: From Scale Bridging to Adaptive Resolution
journal, May 2008

Coupling different levels of resolution in molecular simulations
text, January 2009

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