Coarse graining - Revision history

Carl McBride: Added a recent publication

2018-09-12T11:28:18Z

Added a recent publication

← Older revision		Revision as of 13:28, 12 September 2018
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	*[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/10.1063/1.3663709 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)]		*[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)]


	[[category:computer simulation techniques]]		[[category:computer simulation techniques]]

Carl McBride: Trivial typesetting change to fix link

2016-07-04T12:17:50Z

Trivial typesetting change to fix link

← Older revision		Revision as of 14:17, 4 July 2016
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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 <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
	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. 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.<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>		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 <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>		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>

Mguenza at 22:36, 2 July 2016

2016-07-02T22:36:44Z

← Older revision		Revision as of 00:36, 3 July 2016
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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 <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
	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. 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]].		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 <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>		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>
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	;Related reading		;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/10.1088/0953-8984/16/15/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)]
	*[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/10.1080/00268970701256696 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/10.1063/1.2938860 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)]

Carl McBride: /* References */ Added a recent publication

2012-10-25T10:33:31Z

References: Added a recent publication

← Older revision		Revision as of 12:33, 25 October 2012
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	*[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/10.1063/1.3394863 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/10.1063/1.3663709 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)]



	[[category:computer simulation techniques]]		[[category:computer simulation techniques]]

Carl McBride: Added a recent publication + cite format

2011-12-05T10:48:49Z

Added a recent publication + cite format

← Older revision		Revision as of 12:48, 5 December 2011
Line 1:		Line 1:
	'''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		'''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
	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. 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]].		simulations of large and/or complex modes such as those encountered in studies of [[biological systems]].
	== 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==
	'''~~Related reading~~'''		*[[Multi-particle collision dynamics]]
			== References==
			<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/10.1063/1.2829409 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)]
	*[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/10.1080/00268970701256696 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/10.1063/1.2938860 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)]
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	*[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/10.1063/1.3394862 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/10.1063/1.3394863 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)]



	~~==See also==~~
	*[[Multi-particle collision dynamics]]
	~~== 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]]

Carl McBride: /* Multiscale coarse-graining */ Added some recent publications

2010-04-27T10:11:11Z

Multiscale coarse-graining: Added some recent publications

← Older revision		Revision as of 12:11, 27 April 2010
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	#[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)]		#[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)]
	#[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)]		#[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)]
	#[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)]		'''Related reading'''
	#[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/10.1080/00268970701256696 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/10.1063/1.2938857 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/10.1063/1.2938860 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)]

	==See also==		==See also==
	*[[Multi-particle collision dynamics]]		*[[Multi-particle collision dynamics]]

Nice and Tidy: Added a See also section

2009-11-10T15:11:19Z

Added a See also section

← Older revision		Revision as of 17:11, 10 November 2009
Line 1:		Line 1:
	~~{{Stub-general}}~~
	'''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		'''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. This method is particularly useful when it comes to
Line 10:		Line 9:
	#[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/10.1063/1.2938860 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/10.1063/1.2938857 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)]
			==See also==
			*[[Multi-particle collision dynamics]]
	== References==		== 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/10.1021/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)]

Carl McBride: Added a little more to the introduction.

2008-06-30T14:33:15Z

Added a little more to the introduction.

← Older revision		Revision as of 16:33, 30 June 2008
Line 1:		Line 1:
	{{Stub-general}}		{{Stub-general}}
	'''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		'''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.		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]].
	== 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 (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.

Carl McBride: Added internal link.

2008-06-30T11:54:58Z

Added internal link.

← Older revision		Revision as of 13:54, 30 June 2008
Line 1:		Line 1:
	{{Stub-general}}		{{Stub-general}}
	'''Coarse graining''' is a [[computer simulation techniques \|computer simulation technique]] for reducing the number of degrees of freedom of a system. 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.		to longer time scales or larger effective system sizes.
	== Multiscale coarse-graining==		== Multiscale coarse-graining==

Carl McBride: /* Multiscale coarse-graining */ Added an internal link

2008-06-30T11:53:44Z

Multiscale coarse-graining: Added an internal link

← Older revision		Revision as of 13:53, 30 June 2008
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	to longer time scales or larger effective system sizes.		to longer time scales or larger effective system sizes.
	== 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 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 (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.
	#[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)]		#[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)]
	#[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)]		#[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)]
Line 9:		Line 9:
	#[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/10.1063/1.2938860 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/10.1063/1.2938857 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==		== 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/10.1021/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)]