Coarse graining: Difference between revisions

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'''Coarse graining''' is a [[computer simulation techniques |computer simulation technique]] for reducing the number of [[Degree of freedom | degrees of freedom]] of a system <ref>[http://dx.doi.org/10.1021/la00025a003 B. Smit, K. Esselink, P. A. J. Hilbers, N. M. Van Os, L. A. M. Rupert, and I. Szleifer "Computer simulations of surfactant self-assembly", Langmuir '''9''' pp. 9-11 (1993)]</ref>. Such coarse graining provides access
'''Coarse graining''' is a [[computer simulation techniques |computer simulation technique]] for reducing the number of [[Degree of freedom | degrees of freedom]] of a system. Such coarse graining provides access
to longer time scales or larger effective system sizes. This method is particularly useful when it comes to
to longer time scales or larger effective system sizes.
simulations of large and/or complex modes such as those encountered in studies of [[biological systems]] or synthetic polymers.<ref> [http://dx.doi.org/10.1063/1.2829409 Paola Carbone, Hossein Ali Karimi Varzaneh, Xiaoyu Chen, and Florian Müller-Plathe "Transferability of coarse-grained force fields: The polymer case", Journal of Chemical Physics '''128''' 064904 (2008)]</ref><ref>[http://dx.doi.org/10.1103/PhysRevLett.109.168301 A. J. Clark, J. McCarty, I. Y. Lyubimov, and M. G. Guenza "Thermodynamic Consistency in Variable-Level Coarse Graining of Polymeric Liquids", Physical Review Letters '''109''' 168301 (2012)]</ref>
== Multiscale coarse-graining==
== Multiscale coarse-graining==
Multiscale coarse-graining (MS-CG), developed by  Sergei Izvekov and Gregory Voth (Refs. 1 and 2), employs a variational principle to determine an [[idealised models |interaction potential]] for a coarse grained model from simulations of an [[realistic models |atomically detailed model]] of the same system.
Multiscale coarse-graining (MS-CG), developed by  Sergei Izvekov and Gregory Voth <ref>[http://dx.doi.org/10.1021/jp044629q Sergei Izvekov and Gregory A. Voth "A Multiscale Coarse-Graining Method for Biomolecular Systems", Journal of Physical Chemistry B '''109''' pp. 2469-2473 (2005)] </ref>
#[http://dx.doi.org/10.1021/jp044629q Sergei Izvekov and Gregory A. Voth "A Multiscale Coarse-Graining Method for Biomolecular Systems", Journal of Physical Chemistry B '''109''' pp. 2469-2473 (2005)]  
<ref>[http://dx.doi.org/10.1063/1.2038787  Sergei Izvekov and Gregory A. Voth "Multiscale coarse graining of liquid-state systems",  Journal of Chemical Physics '''123''' 134105 (2005)]</ref>, employs a variational principle to determine an [[idealised models |interaction potential]] for a coarse grained model from simulations of an [[realistic models |atomically detailed model]] of the same system.
#[http://dx.doi.org/10.1063/1.2038787  Sergei Izvekov and Gregory A. Voth "Multiscale coarse graining of liquid-state systems",  Journal of Chemical Physics '''123''' 134105 (2005)]
==See also==
#[http://dx.doi.org/10.1080/00268970701256696 J. -W. Chu;  G. S. Ayton;  S. Izvekov; G. A. Voth "Emerging methods for multiscale simulation of biomolecular systems", Molecular Physics '''105''' pp. 167-175 (2007)]
*[[Multi-particle collision dynamics]]
#[http://dx.doi.org/10.1063/1.2938860 W. G. Noid, Jhih-Wei Chu, Gary S. Ayton, Vinod Krishna, Sergei Izvekov, Gregory A. Voth, Avisek Das, and Hans C. Andersen "The multiscale coarse-graining method. I. A rigorous bridge between atomistic and coarse-grained models", Journal of Chemical Physics '''128''' 244114 (2008)]
== References==
#[http://dx.doi.org/10.1063/1.2938857  W. G. Noid, Pu Liu, Yanting Wang, Jhih-Wei Chu, Gary S. Ayton, Sergei Izvekov, Hans C. Andersen, and Gregory A. Voth "The multiscale coarse-graining method. II. Numerical implementation for coarse-grained molecular models",  Journal of Chemical Physics '''128''' 244115 (2008)]
<references/>
;Related reading
*[http://dx.doi.org/10.1088/0953-8984/16/15/R03 Steve O Nielsen, Carlos F Lopez, Goundla Srinivas and Michael L Klein "Coarse grain models and the computer simulation of soft materials", Journal of Physics: Condensed Matter '''16''' pp. R481-R512 (2004)]
*[http://dx.doi.org/10.1080/00268970701256696 J. -W. Chu;  G. S. Ayton;  S. Izvekov; G. A. Voth "Emerging methods for multiscale simulation of biomolecular systems", Molecular Physics '''105''' pp. 167-175 (2007)]
*[http://dx.doi.org/10.1063/1.2938860 W. G. Noid, Jhih-Wei Chu, Gary S. Ayton, Vinod Krishna, Sergei Izvekov, Gregory A. Voth, Avisek Das, and Hans C. Andersen "The multiscale coarse-graining method. I. A rigorous bridge between atomistic and coarse-grained models", Journal of Chemical Physics '''128''' 244114 (2008)]
*[http://dx.doi.org/10.1063/1.2938857  W. G. Noid, Pu Liu, Yanting Wang, Jhih-Wei Chu, Gary S. Ayton, Sergei Izvekov, Hans C. Andersen, and Gregory A. Voth "The multiscale coarse-graining method. II. Numerical implementation for coarse-grained molecular models",  Journal of Chemical Physics '''128''' 244115 (2008)]
*[http://dx.doi.org/10.1063/1.3173812 Avisek Das and Hans C. Andersen "The multiscale coarse-graining method. III. A test of pairwise additivity of the coarse-grained potential and of new basis functions for the variational calculation", Journal of Chemical Physics '''131''' 034102 (2009)]
*[http://dx.doi.org/10.1063/1.3167797 Vinod Krishna, Will G. Noid, and Gregory A. Voth "The multiscale coarse-graining method. IV. Transferring coarse-grained potentials between temperatures", Journal of Chemical Physics '''131''' 024103 (2009)]
*[http://dx.doi.org/10.1063/1.3394862 Avisek Das and Hans C. Andersen "The multiscale coarse-graining method. V. Isothermal-isobaric ensemble", Journal of Chemical Physics '''132''' 164106 (2010)]
*[http://dx.doi.org/10.1063/1.3394863 Luca Larini, Lanyuan Lu, and Gregory A. Voth "The multiscale coarse-graining method. VI. Implementation of three-body coarse-grained potentials", Journal of Chemical Phhysics '''132''' 164107 (2010)]
*[http://dx.doi.org/10.1063/1.3663709 Joseph F. Rudzinski and W. G. Noid "Coarse-graining entropy, forces, and structures", Journal of Chemical Physics '''135''' 214101 (2011)]
*[http://dx.doi.org/10.1063/1.4759463  Chia-Chun Fu, Pandurang M. Kulkarni, M. Scott Shell, and L. Gary Leal "A test of systematic coarse-graining of molecular dynamics simulations: Thermodynamic properties", Journal of Chemical Physics '''137''' 164106 (2012)]
*[https://doi.org/10.1063/1.5039738 Yining Han, James F. Dama, and Gregory A. Voth "Mesoscopic coarse-grained representations of fluids rigorously derived from atomistic models", Journal of Chemical Physics 149, 044104 (2018)]
 


== References==
#[http://dx.doi.org/10.1021/la00025a003 B. Smit, K. Esselink, P. A. J. Hilbers, N. M. Van Os, L. A. M. Rupert, and I. Szleifer "Computer simulations of surfactant self-assembly", Langmuir '''9''' pp. 9-11 (1993)]
#[http://dx.doi.org/10.1088/0953-8984/16/15/R03 Steve O Nielsen, Carlos F Lopez, Goundla Srinivas and Michael L Klein "Coarse grain models and the computer simulation of soft materials", Journal of Physics: Condensed Matter '''16''' pp. R481-R512 (2004)]
#[http://dx.doi.org/10.1063/1.2829409 Paola Carbone, Hossein Ali Karimi Varzaneh, Xiaoyu Chen, and Florian Müller-Plathe "Transferability of coarse-grained force fields: The polymer case", Journal of Chemical Physics '''128''' 064904 (2008)]
[[category:computer simulation techniques]]
[[category:computer simulation techniques]]

Latest revision as of 12:28, 12 September 2018

Coarse graining is a computer simulation technique for reducing the number of degrees of freedom of a system [1]. Such coarse graining provides access to longer time scales or larger effective system sizes. This method is particularly useful when it comes to simulations of large and/or complex modes such as those encountered in studies of biological systems or synthetic polymers.[2][3]

Multiscale coarse-graining[edit]

Multiscale coarse-graining (MS-CG), developed by Sergei Izvekov and Gregory Voth [4] [5], employs a variational principle to determine an interaction potential for a coarse grained model from simulations of an atomically detailed model of the same system.

See also[edit]

References[edit]

Related reading