skip to main content
OSTI.GOV title logo U.S. Department of Energy
Office of Scientific and Technical Information

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

Authors:
 [1];  [2]
  1. Ames Laboratory, Iowa State University, Ames, Iowa 50011, USA
  2. Ames Laboratory, Iowa State University, Ames, Iowa 50011, USA, Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa 50011, USA
Publication Date:
Sponsoring Org.:
USDOE
OSTI Identifier:
1224271
Grant/Contract Number:  
AL-08-330-039
Resource Type:
Journal Article: 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.
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
Markutsya, Sergiy, and Lamm, Monica H. 2014. "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.
@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},
url = {https://www.osti.gov/biblio/1224271}, journal = {The Journal of Chemical Physics},
issn = {0021-9606},
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}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record at https://doi.org/10.1063/1.4898625

Citation Metrics:
Cited by: 19 works
Citation information provided by
Web of Science

Save / Share:

Works referenced in this record:

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


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


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


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


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


Variational Treatment of Hydrodynamic Interaction in Polymers
journal, June 1969


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