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. 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 | ||
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#[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)] | ||
Revision as of 17:11, 10 November 2009
Coarse graining is a computer simulation technique for reducing the number of 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 simulations of large and/or complex modes such as those encountered in studies of biological systems.
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 atomically detailed model of the same system.
- Sergei Izvekov and Gregory A. Voth "A Multiscale Coarse-Graining Method for Biomolecular Systems", Journal of Physical Chemistry B 109 pp. 2469-2473 (2005)
- Sergei Izvekov and Gregory A. Voth "Multiscale coarse graining of liquid-state systems", Journal of Chemical Physics 123 134105 (2005)
- 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)
- 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)
- 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
References
- 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)
- 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)
- 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)