The geometry of generalized force matching and related information metrics in coarse-graining of molecular systems

Kalligiannaki, Evangelia; Harmandaris, Vagelis; Katsoulakis, Markos A.; Plecháč, Petr

doi:10.1063/1.4928857

Title: The geometry of generalized force matching and related information metrics in coarse-graining of molecular systems

Authors:

Kalligiannaki, Evangelia ^[1]; Harmandaris, Vagelis ^[2]; Katsoulakis, Markos A. ^[3]; Plecháč, Petr ^[4]

Department of Mathematics and Applied Mathematics, University of Crete, 70013 Heraklion, Greece
Department of Mathematics and Applied Mathematics, University of Crete, 70013 Heraklion, Greece, Institute of Applied and Computational Mathematics (IACM), Foundation for Research and Technology Hellas (FORTH), IACM/FORTH, GR-71110 Heraklion, Greece
Department of Mathematics and Statistics, University of Massachusetts, Amherst, Massachusetts 01003, USA
Department of Mathematical Sciences, University of Delaware, Newark, Delaware 19716, USA

Publication Date:: Fri Aug 28 00:00:00 EDT 2015

Sponsoring Org.:: USDOE

OSTI Identifier:: 1229632

Grant/Contract Number:: SC0010723; SC-0007046

Resource Type:: Publisher's Accepted Manuscript

Journal Name:: Journal of Chemical Physics

Additional Journal Information:: Journal Name: Journal of Chemical Physics Journal Volume: 143 Journal Issue: 8; Journal ID: ISSN 0021-9606

Publisher:: American Institute of Physics

Country of Publication:: United States

Language:: English

Citation Formats


                    Kalligiannaki, Evangelia, Harmandaris, Vagelis, Katsoulakis, Markos A., and Plecháč, Petr. The geometry of generalized force matching and related information metrics in coarse-graining of molecular systems.  United States: N. p., 2015. 
Web.  doi:10.1063/1.4928857.

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                    Kalligiannaki, Evangelia, Harmandaris, Vagelis, Katsoulakis, Markos A., & Plecháč, Petr. The geometry of generalized force matching and related information metrics in coarse-graining of molecular systems.  United States.  https://doi.org/10.1063/1.4928857

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                    Kalligiannaki, Evangelia, Harmandaris, Vagelis, Katsoulakis, Markos A., and Plecháč, Petr. Fri .  
"The geometry of generalized force matching and related information metrics in coarse-graining of molecular systems".  United States.  https://doi.org/10.1063/1.4928857.

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@article{osti_1229632,

  title        = {The geometry of generalized force matching and related information metrics in coarse-graining of molecular systems},

  author       = {Kalligiannaki, Evangelia and Harmandaris, Vagelis and Katsoulakis, Markos A. and Plecháč, Petr},

  abstractNote = {},

  doi          = {10.1063/1.4928857},

  journal      = {Journal of Chemical Physics},

  number       = 8,

  volume       = 143,

  place        = {United States},

  year         = {Fri Aug 28 00:00:00 EDT 2015},

  month        = {Fri Aug 28 00:00:00 EDT 2015}

}

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Title: The geometry of generalized force matching and related information metrics in coarse-graining of molecular systems

Citation Formats

On the Reduction of Molecular Degrees of Freedom in Computer Simulations book, February 2004

Uncrossability constraints in mesoscopic polymer melt simulations: Non-Rouse behavior of C120H242 journal, August 2001

Multilevel coarse graining and nano-pattern discovery in many particle stochastic systems journal, March 2012

A stochastic optimization approach to coarse-graining using a relative-entropy framework journal, January 2013

Multiscale coarse graining of liquid-state systems journal, October 2005

Blue Moon Sampling, Vectorial Reaction Coordinates, and Unbiased Constrained Dynamics journal, September 2005

Simulation of polymer melts. II. From coarse-grained models back to atomistic description journal, February 1998

Free energy from constrained molecular dynamics journal, November 1998

From Mesoscale Back to Microscale: Reconstruction Schemes for Coarse-Grained Stochastic Lattice Systems journal, January 2010

The calculation of free-energy differences by constrained molecular-dynamics simulations journal, September 1998

Anomalous waterlike behavior in spherically-symmetric water models optimized with the relative entropy journal, January 2009

An analytical coarse-graining method which preserves the free energy, structural correlations, and thermodynamic state of polymer melts from the atomistic to the mesoscale journal, May 2014

Predicting polymer dynamics at multiple length and time scales journal, January 2009

Thermodynamic integration of the free energy along a reaction coordinate in Cartesian coordinates journal, May 2000

Coarse-grained interactions in polymer melts: A variational approach journal, October 2001

Effective Force Field for Liquid Hydrogen Fluoride from Ab Initio Molecular Dynamics Simulation Using the Force-Matching Method † journal, April 2005

Dynamics of Polystyrene Melts through Hierarchical Multiscale Simulations journal, February 2009

Efficient, Regularized, and Scalable Algorithms for Multiscale Coarse-Graining journal, January 2010

Hierarchical Modeling of Polystyrene: From Atomistic to Coarse-Grained Simulations journal, September 2006

A uniqueness theorem for fluid pair correlation functions journal, September 1974

Probability book, January 1996

Quantitative study of equilibrium and non-equilibrium polymer dynamics through systematic hierarchical coarse-graining simulations journal, February 2014

Numerical and Statistical Methods for the Coarse-Graining of Many-Particle Stochastic Systems journal, July 2008

Coarse-graining entropy, forces, and structures journal, December 2011

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

Coarse-Graining in Polymer Simulation: From the Atomistic to the Mesoscopic Scale and Back journal, September 2002

The relative entropy is fundamental to multiscale and inverse thermodynamic problems journal, October 2008

Hierarchical simulations of hybrid polymer–solid materials journal, January 2013

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

Empirical potential Monte Carlo simulation of fluid structure journal, January 1996

Obtaining fully dynamic coarse-grained models from MD journal, January 2011

Crossover from the Rouse to the Entangled Polymer Melt Regime: Signals from Long, Detailed Atomistic Molecular Dynamics Simulations, Supported by Rheological Experiments journal, February 2003

Diffusion Maps, Reduction Coordinates, and Low Dimensional Representation of Stochastic Systems journal, January 2008

Statistical Mechanics of Fluid Mixtures journal, May 1935

The multiscale coarse-graining method. I. A rigorous bridge between atomistic and coarse-grained models journal, June 2008

Information-theoretic tools for parametrized coarse-graining of non-equilibrium extended systems journal, August 2013

Quantitative Analysis on the Validity of a Coarse-Grained Model for Nonequilibrium Polymeric Liquids under Flow journal, April 2010

On the Reduction of Molecular Degrees of Freedom in Computer Simulations
book, February 2004

Uncrossability constraints in mesoscopic polymer melt simulations: Non-Rouse behavior of C120H242
journal, August 2001

Multilevel coarse graining and nano-pattern discovery in many particle stochastic systems
journal, March 2012

A stochastic optimization approach to coarse-graining using a relative-entropy framework
journal, January 2013

Multiscale coarse graining of liquid-state systems
journal, October 2005

Blue Moon Sampling, Vectorial Reaction Coordinates, and Unbiased Constrained Dynamics
journal, September 2005

Simulation of polymer melts. II. From coarse-grained models back to atomistic description
journal, February 1998

Free energy from constrained molecular dynamics
journal, November 1998

From Mesoscale Back to Microscale: Reconstruction Schemes for Coarse-Grained Stochastic Lattice Systems
journal, January 2010

The calculation of free-energy differences by constrained molecular-dynamics simulations
journal, September 1998

Anomalous waterlike behavior in spherically-symmetric water models optimized with the relative entropy
journal, January 2009

An analytical coarse-graining method which preserves the free energy, structural correlations, and thermodynamic state of polymer melts from the atomistic to the mesoscale
journal, May 2014

Predicting polymer dynamics at multiple length and time scales
journal, January 2009

Thermodynamic integration of the free energy along a reaction coordinate in Cartesian coordinates
journal, May 2000

Coarse-grained interactions in polymer melts: A variational approach
journal, October 2001

Effective Force Field for Liquid Hydrogen Fluoride from Ab Initio Molecular Dynamics Simulation Using the Force-Matching Method ^†
journal, April 2005

Dynamics of Polystyrene Melts through Hierarchical Multiscale Simulations
journal, February 2009

Efficient, Regularized, and Scalable Algorithms for Multiscale Coarse-Graining
journal, January 2010

Hierarchical Modeling of Polystyrene: From Atomistic to Coarse-Grained Simulations
journal, September 2006

A uniqueness theorem for fluid pair correlation functions
journal, September 1974

Probability
book, January 1996

Quantitative study of equilibrium and non-equilibrium polymer dynamics through systematic hierarchical coarse-graining simulations
journal, February 2014

Numerical and Statistical Methods for the Coarse-Graining of Many-Particle Stochastic Systems
journal, July 2008

Coarse-graining entropy, forces, and structures
journal, December 2011

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

Coarse-Graining in Polymer Simulation: From the Atomistic to the Mesoscopic Scale and Back
journal, September 2002

The relative entropy is fundamental to multiscale and inverse thermodynamic problems
journal, October 2008

Hierarchical simulations of hybrid polymer–solid materials
journal, January 2013

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

Empirical potential Monte Carlo simulation of fluid structure
journal, January 1996

Obtaining fully dynamic coarse-grained models from MD
journal, January 2011

Crossover from the Rouse to the Entangled Polymer Melt Regime: Signals from Long, Detailed Atomistic Molecular Dynamics Simulations, Supported by Rheological Experiments
journal, February 2003

Diffusion Maps, Reduction Coordinates, and Low Dimensional Representation of Stochastic Systems
journal, January 2008

Statistical Mechanics of Fluid Mixtures
journal, May 1935

The multiscale coarse-graining method. I. A rigorous bridge between atomistic and coarse-grained models
journal, June 2008

Information-theoretic tools for parametrized coarse-graining of non-equilibrium extended systems
journal, August 2013

Quantitative Analysis on the Validity of a Coarse-Grained Model for Nonequilibrium Polymeric Liquids under Flow
journal, April 2010