A coarse-graining approach for molecular simulation that retains the dynamics of the all-atom reference system by implementing hydrodynamic interactions
- Authors:
-
- 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:
- 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}
}
Free Publicly Available Full Text
Publisher's Version of Record at https://doi.org/10.1063/1.4898625
Other availability
Cited by: 19 works
Citation information provided by
Web of Science
Web of Science
Save to My Library
You must Sign In or Create an Account in order to save documents to your library.
Works referenced in this record:
Modeling diffusive dynamics in adaptive resolution simulation of liquid water
journal, January 2008
- Matysiak, Silvina; Clementi, Cecilia; Praprotnik, Matej
- The Journal of Chemical Physics, Vol. 128, Issue 2
Concerted Interconversion between Ionic Lock Substates of the β2 Adrenergic Receptor Revealed by Microsecond Timescale Molecular Dynamics
journal, January 2010
- Romo, Tod D.; Grossfield, Alan; Pitman, Michael C.
- Biophysical Journal, Vol. 98, Issue 1
A Solvent-Free Coarse Grain Model for Crystalline and Amorphous Cellulose Fibrils
journal, July 2011
- Srinivas, Goundla; Cheng, Xiaolin; Smith, Jeremy C.
- Journal of Chemical Theory and Computation, Vol. 7, Issue 8
Microsecond Simulations of Spontaneous Methane Hydrate Nucleation and Growth
journal, October 2009
- Walsh, M. R.; Koh, C. A.; Sloan, E. D.
- Science, Vol. 326, Issue 5956
Multiscale coarse graining of liquid-state systems
journal, October 2005
- Izvekov, Sergei; Voth, Gregory A.
- The Journal of Chemical Physics, Vol. 123, Issue 13
A coarse-grained model for β-d-glucose based on force matching
journal, March 2012
- Markutsya, Sergiy; Kholod, Yana A.; Devarajan, Ajitha
- Theoretical Chemistry Accounts, Vol. 131, Issue 3
Construction of Langevin forces in the simulation of hydrodynamic interaction
journal, July 1986
- Fixman, Marshall
- Macromolecules, Vol. 19, Issue 4
Atomic-Level Characterization of the Structural Dynamics of Proteins
journal, October 2010
- Shaw, D. E.; Maragakis, P.; Lindorff-Larsen, K.
- Science, Vol. 330, Issue 6002
An O(N2) approximation for hydrodynamic interactions in Brownian dynamics simulations
journal, March 2009
- Geyer, Tihamér; Winter, Uwe
- The Journal of Chemical Physics, Vol. 130, Issue 11
Fast Parallel Algorithms for Short-Range Molecular Dynamics
journal, March 1995
- Plimpton, Steve
- Journal of Computational Physics, Vol. 117, Issue 1
Predicting polymer dynamics at multiple length and time scales
journal, January 2009
- Harmandaris, Vagelis A.; Kremer, Kurt
- Soft Matter, Vol. 5, Issue 20
Time versus temperature rescaling for coarse grain molecular dynamics simulations
journal, March 2012
- Accary, J. B.; Teboul, V.
- The Journal of Chemical Physics, Vol. 136, Issue 9
Comparison of simple potential functions for simulating liquid water
journal, July 1983
- Jorgensen, William L.; Chandrasekhar, Jayaraman; Madura, Jeffry D.
- The Journal of Chemical Physics, Vol. 79, Issue 2
The MARTINI Coarse-Grained Force Field: Extension to Proteins
journal, April 2008
- Monticelli, Luca; Kandasamy, Senthil K.; Periole, Xavier
- Journal of Chemical Theory and Computation, Vol. 4, Issue 5
Brownian Dynamics Simulation of Nucleocytoplasmic Transport: A Coarse-Grained Model for the Functional State of the Nuclear Pore Complex
journal, June 2011
- Moussavi-Baygi, Ruhollah; Jamali, Yousef; Karimi, Reza
- PLoS Computational Biology, Vol. 7, Issue 6
Brownian dynamics of cytochrome c and cytochrome c peroxidase association
journal, July 1988
- Northrup, S.; Boles, J.; Reynolds, J.
- Science, Vol. 241, Issue 4861
Coarse-Graining in Polymer Simulation: From the Atomistic to the Mesoscopic Scale and Back
journal, September 2002
- Müller-Plathe, Florian
- ChemPhysChem, Vol. 3, Issue 9
Modeling real dynamics in the coarse-grained representation of condensed phase systems
journal, October 2006
- Izvekov, Sergei; Voth, Gregory A.
- The Journal of Chemical Physics, Vol. 125, Issue 15
Coarse-Graining Approach to Infer Mesoscale Interaction Potentials from Atomistic Interactions for Aggregating Systems
journal, November 2012
- Markutsya, Sergiy; Fox, Rodney O.; Subramaniam, Shankar
- Industrial & Engineering Chemistry Research, Vol. 51, Issue 49
Rate theory for solids. IV. Classical Brownian-motion model
journal, July 1974
- Weiner, J. H.; Forman, R. E.
- Physical Review B, Vol. 10, Issue 2
Calculating hydrodynamic properties of DNA through a second-order Brownian dynamics algorithm
journal, March 1992
- Chirico, Giuseppe; Langowski, Joerg
- Macromolecules, Vol. 25, Issue 2
Obtaining fully dynamic coarse-grained models from MD
journal, January 2011
- Español, Pep; Zúñiga, Ignacio
- Physical Chemistry Chemical Physics, Vol. 13, Issue 22
Structure and Dynamics of the TIP3P, SPC, and SPC/E Water Models at 298 K
journal, November 2001
- Mark, Pekka; Nilsson, Lennart
- The Journal of Physical Chemistry A, Vol. 105, Issue 43
Striking Effects of Hydrodynamic Interactions on the Simulated Diffusion and Folding of Proteins
journal, January 2009
- Frembgen-Kesner, Tamara; Elcock, Adrian H.
- Journal of Chemical Theory and Computation, Vol. 5, Issue 2
A Lipid Pathway for Ligand Binding Is Necessary for a Cannabinoid G Protein-coupled Receptor
journal, March 2010
- Hurst, Dow P.; Grossfield, Alan; Lynch, Diane L.
- Journal of Biological Chemistry, Vol. 285, Issue 23
The fluctuation-dissipation theorem
journal, January 1966
- Kubo, R.
- Reports on Progress in Physics, Vol. 29, Issue 1
Large-Scale Molecular Dynamics Simulations of Self-Assembling Systems
journal, August 2008
- Klein, M. L.; Shinoda, W.
- Science, Vol. 321, Issue 5890
Multiscale Simulation of Soft Matter: From Scale Bridging to Adaptive Resolution
journal, May 2008
- Praprotnik, Matej; Site, Luigi Delle; Kremer, Kurt
- Annual Review of Physical Chemistry, Vol. 59, Issue 1
A stochastic optimization approach to coarse-graining using a relative-entropy framework
journal, January 2013
- Bilionis, Ilias; Zabaras, Nicholas
- The Journal of Chemical Physics, Vol. 138, Issue 4
Coarse-grained single-particle dynamics in two-dimensional solids and liquids
journal, July 2008
- Silbermann, Jörg R.; Schoen, Martin; Klapp, Sabine H. L.
- Physical Review E, Vol. 78, Issue 1
LINCS: A linear constraint solver for molecular simulations
journal, September 1997
- Hess, Berk; Bekker, Henk; Berendsen, Herman J. C.
- Journal of Computational Chemistry, Vol. 18, Issue 12
The multiscale coarse-graining method. V. Isothermal-isobaric ensemble
journal, April 2010
- Das, Avisek; Andersen, Hans C.
- The Journal of Chemical Physics, Vol. 132, Issue 16
Particle mesh Ewald: An N ⋅log( N ) method for Ewald sums in large systems
journal, June 1993
- Darden, Tom; York, Darrin; Pedersen, Lee
- The Journal of Chemical Physics, Vol. 98, Issue 12
Brownian dynamics simulation of bead–rod chains under shear with hydrodynamic interaction
journal, October 1999
- Petera, D.; Muthukumar, M.
- The Journal of Chemical Physics, Vol. 111, Issue 16
A coarse-grained molecular dynamics model for crystalline solids
journal, August 2010
- Li, Xiantao
- International Journal for Numerical Methods in Engineering, Vol. 83, Issue 8-9
Reintroducing explicit solvent to a solvent-free coarse-grained model
journal, August 2011
- Kim, Seung Ha; Lamm, Monica H.
- Physical Review E, Vol. 84, Issue 2
Calculation of effective interaction potentials from radial distribution functions: A reverse Monte Carlo approach
journal, October 1995
- Lyubartsev, Alexander P.; Laaksonen, Aatto
- Physical Review E, Vol. 52, Issue 4
Coarse Grained Model for Semiquantitative Lipid Simulations
journal, January 2004
- Marrink, Siewert J.; de Vries, Alex H.; Mark, Alan E.
- The Journal of Physical Chemistry B, Vol. 108, Issue 2
Coarse-Grained Biomolecular Simulation with REACH: Realistic Extension Algorithm via Covariance Hessian
journal, November 2007
- Moritsugu, Kei; Smith, Jeremy C.
- Biophysical Journal, Vol. 93, Issue 10
Brownian dynamics with hydrodynamic interactions
journal, August 1978
- Ermak, Donald L.; McCammon, J. A.
- The Journal of Chemical Physics, Vol. 69, Issue 4
Coarse-grained model for phospholipid/cholesterol bilayer
journal, November 2004
- Murtola, Teemu; Falck, Emma; Patra, Michael
- The Journal of Chemical Physics, Vol. 121, Issue 18
Effective Force Field for Liquid Hydrogen Fluoride from Ab Initio Molecular Dynamics Simulation Using the Force-Matching Method †
journal, April 2005
- Izvekov, Sergei; Voth, Gregory A.
- The Journal of Physical Chemistry B, Vol. 109, Issue 14
Computer simulation study of fullerene translocation through lipid membranes
journal, May 2008
- Wong-Ekkabut, Jirasak; Baoukina, Svetlana; Triampo, Wannapong
- Nature Nanotechnology, Vol. 3, Issue 6
The MARTINI Force Field: Coarse Grained Model for Biomolecular Simulations
journal, July 2007
- Marrink, Siewert J.; Risselada, H. Jelger; Yefimov, Serge
- The Journal of Physical Chemistry B, Vol. 111, Issue 27
The multiscale coarse-graining method. II. Numerical implementation for coarse-grained molecular models
journal, June 2008
- Noid, W. G.; Liu, Pu; Wang, Yanting
- The Journal of Chemical Physics, Vol. 128, Issue 24
Nonlinear generalized Langevin equations
journal, November 1973
- Zwanzig, Robert
- Journal of Statistical Physics, Vol. 9, Issue 3
CHARMM Additive All-Atom Force Field for Glycosidic Linkages between Hexopyranoses
journal, August 2009
- Guvench, Olgun; Hatcher, Elizabeth; Venable, Richard M.
- Journal of Chemical Theory and Computation, Vol. 5, Issue 9
Settle: An analytical version of the SHAKE and RATTLE algorithm for rigid water models
journal, October 1992
- Miyamoto, Shuichi; Kollman, Peter A.
- Journal of Computational Chemistry, Vol. 13, Issue 8
The relative entropy is fundamental to multiscale and inverse thermodynamic problems
journal, October 2008
- Shell, M. Scott
- The Journal of Chemical Physics, Vol. 129, Issue 14
Systematic coarse-graining of potential energy landscapes and dynamics in liquids
journal, August 2012
- Shell, M. Scott
- The Journal of Chemical Physics, Vol. 137, Issue 8
Numerical integration of the Langevin equation: Monte Carlo simulation
journal, April 1980
- Ermak, Donald L.; Buckholz, Helen
- Journal of Computational Physics, Vol. 35, Issue 2
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
- Lemons, Don S.; Gythiel, Anthony
- American Journal of Physics, Vol. 65, Issue 11
Deriving effective mesoscale potentials from atomistic simulations: Mesoscale Potentials from Atomistic Simulations
journal, August 2003
- Reith, Dirk; Pütz, Mathias; Müller-Plathe, Florian
- Journal of Computational Chemistry, Vol. 24, Issue 13
Über die von der molekularkinetischen Theorie der Wärme geforderte Bewegung von in ruhenden Flüssigkeiten suspendierten Teilchen
journal, January 1905
- Einstein, A.
- Annalen der Physik, Vol. 322, Issue 8
Variational Treatment of Hydrodynamic Interaction in Polymers
journal, June 1969
- Rotne, Jens; Prager, Stephen
- The Journal of Chemical Physics, Vol. 50, Issue 11
First-principle approach to rescale the dynamics of simulated coarse-grained macromolecular liquids
journal, September 2011
- Lyubimov, I.; Guenza, M. G.
- Physical Review E, Vol. 84, Issue 3
The multiscale coarse-graining method. I. A rigorous bridge between atomistic and coarse-grained models
journal, June 2008
- Noid, W. G.; Chu, Jhih-Wei; Ayton, Gary S.
- The Journal of Chemical Physics, Vol. 128, Issue 24