A coarse-graining approach for molecular simulation that retains the dynamics of the all-atom reference system by implementing hydrodynamic interactions

Markutsya, Sergiy; Lamm, Monica H.

doi:10.1063/1.4898625

Title: A coarse-graining approach for molecular simulation that retains the dynamics of the all-atom reference system by implementing hydrodynamic interactions

Authors:

Markutsya, Sergiy ^[1]; Lamm, Monica H. ^[2]

Ames Laboratory, Iowa State University, Ames, Iowa 50011, USA
Ames Laboratory, Iowa State University, Ames, Iowa 50011, USA, Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa 50011, USA

Publication Date:: Tue Nov 04 00:00:00 EST 2014

Sponsoring Org.:: USDOE

OSTI Identifier:: 1224271

Grant/Contract Number:: AL-08-330-039

Resource Type:: Publisher's Accepted Manuscript

Journal Name:: The Journal of Chemical Physics

Additional Journal Information:: Journal Name: The Journal of Chemical Physics Journal Volume: 141 Journal Issue: 17; Journal ID: ISSN 0021-9606

Publisher:: American Institute of Physics

Country of Publication:: United States

Language:: English

Citation Formats


                    Markutsya, Sergiy, and Lamm, Monica H. A coarse-graining approach for molecular simulation that retains the dynamics of the all-atom reference system by implementing hydrodynamic interactions.  United States: N. p., 2014. 
Web.  doi:10.1063/1.4898625.

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                    Markutsya, Sergiy, & Lamm, Monica H. A coarse-graining approach for molecular simulation that retains the dynamics of the all-atom reference system by implementing hydrodynamic interactions.  United States.  https://doi.org/10.1063/1.4898625

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                    Markutsya, Sergiy, and Lamm, Monica H. Tue .  
"A coarse-graining approach for molecular simulation that retains the dynamics of the all-atom reference system by implementing hydrodynamic interactions".  United States.  https://doi.org/10.1063/1.4898625.

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@article{osti_1224271,

  title        = {A coarse-graining approach for molecular simulation that retains the dynamics of the all-atom reference system by implementing hydrodynamic interactions},

  author       = {Markutsya, Sergiy and Lamm, Monica H.},

  abstractNote = {},

  doi          = {10.1063/1.4898625},

  journal      = {The Journal of Chemical Physics},

  number       = 17,

  volume       = 141,

  place        = {United States},

  year         = {Tue Nov 04 00:00:00 EST 2014},

  month        = {Tue Nov 04 00:00:00 EST 2014}

}

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Title: A coarse-graining approach for molecular simulation that retains the dynamics of the all-atom reference system by implementing hydrodynamic interactions

Citation Formats

Modeling diffusive dynamics in adaptive resolution simulation of liquid water journal, January 2008

Concerted Interconversion between Ionic Lock Substates of the β2 Adrenergic Receptor Revealed by Microsecond Timescale Molecular Dynamics journal, January 2010

A Solvent-Free Coarse Grain Model for Crystalline and Amorphous Cellulose Fibrils journal, July 2011

Microsecond Simulations of Spontaneous Methane Hydrate Nucleation and Growth journal, October 2009

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Construction of Langevin forces in the simulation of hydrodynamic interaction journal, July 1986

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An O(N2) approximation for hydrodynamic interactions in Brownian dynamics simulations journal, March 2009

Fast Parallel Algorithms for Short-Range Molecular Dynamics journal, March 1995

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

Time versus temperature rescaling for coarse grain molecular dynamics simulations journal, March 2012

Comparison of simple potential functions for simulating liquid water journal, July 1983

The MARTINI Coarse-Grained Force Field: Extension to Proteins journal, April 2008

Brownian Dynamics Simulation of Nucleocytoplasmic Transport: A Coarse-Grained Model for the Functional State of the Nuclear Pore Complex journal, June 2011

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

Modeling real dynamics in the coarse-grained representation of condensed phase systems journal, October 2006

Coarse-Graining Approach to Infer Mesoscale Interaction Potentials from Atomistic Interactions for Aggregating Systems journal, November 2012

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Calculating hydrodynamic properties of DNA through a second-order Brownian dynamics algorithm journal, March 1992

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

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Striking Effects of Hydrodynamic Interactions on the Simulated Diffusion and Folding of Proteins journal, January 2009

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

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The multiscale coarse-graining method. V. Isothermal-isobaric ensemble journal, April 2010

Particle mesh Ewald: An N ⋅log( N ) method for Ewald sums in large systems journal, June 1993

Brownian dynamics simulation of bead–rod chains under shear with hydrodynamic interaction journal, October 1999

A coarse-grained molecular dynamics model for crystalline solids journal, August 2010

Reintroducing explicit solvent to a solvent-free coarse-grained model journal, August 2011

Calculation of effective interaction potentials from radial distribution functions: A reverse Monte Carlo approach journal, October 1995

Coarse Grained Model for Semiquantitative Lipid Simulations journal, January 2004

Coarse-Grained Biomolecular Simulation with REACH: Realistic Extension Algorithm via Covariance Hessian journal, November 2007

Brownian dynamics with hydrodynamic interactions journal, August 1978

Coarse-grained model for phospholipid/cholesterol bilayer journal, November 2004

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

Computer simulation study of fullerene translocation through lipid membranes journal, May 2008

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

The multiscale coarse-graining method. II. Numerical implementation for coarse-grained molecular models journal, June 2008

Nonlinear generalized Langevin equations journal, November 1973

CHARMM Additive All-Atom Force Field for Glycosidic Linkages between Hexopyranoses journal, August 2009

Settle: An analytical version of the SHAKE and RATTLE algorithm for rigid water models journal, October 1992

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

Systematic coarse-graining of potential energy landscapes and dynamics in liquids journal, August 2012

Numerical integration of the Langevin equation: Monte Carlo simulation journal, April 1980

Paul Langevin’s 1908 paper “On the Theory of Brownian Motion” [“Sur la théorie du mouvement brownien,” C. R. Acad. Sci. (Paris) 146 , 530–533 (1908)] journal, November 1997

Deriving effective mesoscale potentials from atomistic simulations: Mesoscale Potentials from Atomistic Simulations journal, August 2003

Über die von der molekularkinetischen Theorie der Wärme geforderte Bewegung von in ruhenden Flüssigkeiten suspendierten Teilchen journal, January 1905

Variational Treatment of Hydrodynamic Interaction in Polymers journal, June 1969

First-principle approach to rescale the dynamics of simulated coarse-grained macromolecular liquids journal, September 2011

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

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journal, January 2008

Concerted Interconversion between Ionic Lock Substates of the β2 Adrenergic Receptor Revealed by Microsecond Timescale Molecular Dynamics
journal, January 2010

A Solvent-Free Coarse Grain Model for Crystalline and Amorphous Cellulose Fibrils
journal, July 2011

Microsecond Simulations of Spontaneous Methane Hydrate Nucleation and Growth
journal, October 2009

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

A coarse-grained model for β-d-glucose based on force matching
journal, March 2012

Construction of Langevin forces in the simulation of hydrodynamic interaction
journal, July 1986

Atomic-Level Characterization of the Structural Dynamics of Proteins
journal, October 2010

An O(N2) approximation for hydrodynamic interactions in Brownian dynamics simulations
journal, March 2009

Fast Parallel Algorithms for Short-Range Molecular Dynamics
journal, March 1995

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

Time versus temperature rescaling for coarse grain molecular dynamics simulations
journal, March 2012

Comparison of simple potential functions for simulating liquid water
journal, July 1983

The MARTINI Coarse-Grained Force Field: Extension to Proteins
journal, April 2008

Brownian Dynamics Simulation of Nucleocytoplasmic Transport: A Coarse-Grained Model for the Functional State of the Nuclear Pore Complex
journal, June 2011

Brownian dynamics of cytochrome c and cytochrome c peroxidase association
journal, July 1988

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

Modeling real dynamics in the coarse-grained representation of condensed phase systems
journal, October 2006

Coarse-Graining Approach to Infer Mesoscale Interaction Potentials from Atomistic Interactions for Aggregating Systems
journal, November 2012

Rate theory for solids. IV. Classical Brownian-motion model
journal, July 1974

Calculating hydrodynamic properties of DNA through a second-order Brownian dynamics algorithm
journal, March 1992

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

Structure and Dynamics of the TIP3P, SPC, and SPC/E Water Models at 298 K
journal, November 2001

Striking Effects of Hydrodynamic Interactions on the Simulated Diffusion and Folding of Proteins
journal, January 2009

A Lipid Pathway for Ligand Binding Is Necessary for a Cannabinoid G Protein-coupled Receptor
journal, March 2010

The fluctuation-dissipation theorem
journal, January 1966

Large-Scale Molecular Dynamics Simulations of Self-Assembling Systems
journal, August 2008

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

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

Coarse-grained single-particle dynamics in two-dimensional solids and liquids
journal, July 2008

LINCS: A linear constraint solver for molecular simulations
journal, September 1997

The multiscale coarse-graining method. V. Isothermal-isobaric ensemble
journal, April 2010

Particle mesh Ewald: An N ⋅log( N ) method for Ewald sums in large systems
journal, June 1993

Brownian dynamics simulation of bead–rod chains under shear with hydrodynamic interaction
journal, October 1999

A coarse-grained molecular dynamics model for crystalline solids
journal, August 2010

Reintroducing explicit solvent to a solvent-free coarse-grained model
journal, August 2011

Calculation of effective interaction potentials from radial distribution functions: A reverse Monte Carlo approach
journal, October 1995

Coarse Grained Model for Semiquantitative Lipid Simulations
journal, January 2004

Coarse-Grained Biomolecular Simulation with REACH: Realistic Extension Algorithm via Covariance Hessian
journal, November 2007

Brownian dynamics with hydrodynamic interactions
journal, August 1978

Coarse-grained model for phospholipid/cholesterol bilayer
journal, November 2004

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

Computer simulation study of fullerene translocation through lipid membranes
journal, May 2008

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

The multiscale coarse-graining method. II. Numerical implementation for coarse-grained molecular models
journal, June 2008

Nonlinear generalized Langevin equations
journal, November 1973

CHARMM Additive All-Atom Force Field for Glycosidic Linkages between Hexopyranoses
journal, August 2009

Settle: An analytical version of the SHAKE and RATTLE algorithm for rigid water models
journal, October 1992

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

Systematic coarse-graining of potential energy landscapes and dynamics in liquids
journal, August 2012

Numerical integration of the Langevin equation: Monte Carlo simulation
journal, April 1980

Paul Langevin’s 1908 paper “On the Theory of Brownian Motion” [“Sur la théorie du mouvement brownien,” C. R. Acad. Sci. (Paris) 146 , 530–533 (1908)]
journal, November 1997

Deriving effective mesoscale potentials from atomistic simulations: Mesoscale Potentials from Atomistic Simulations
journal, August 2003

Über die von der molekularkinetischen Theorie der Wärme geforderte Bewegung von in ruhenden Flüssigkeiten suspendierten Teilchen
journal, January 1905

Variational Treatment of Hydrodynamic Interaction in Polymers
journal, June 1969

First-principle approach to rescale the dynamics of simulated coarse-grained macromolecular liquids
journal, September 2011

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