Coarse graining: Difference between revisions
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'''Coarse graining''' is a technique for reducing the number of degrees of freedom of a system. | '''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 | |||
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 (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> | |||
<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. | |||
==See also== | |||
*[[Multi-particle collision dynamics]] | |||
== References== | == 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/10.1080/00268970701256696 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)] | |||
[[category:computer simulation techniques]] | [[category:computer simulation techniques]] | ||
Latest revision as of 13:28, 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]
- ↑ 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)
- ↑ 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)
- ↑ 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)
- ↑ 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)
- Related reading
- 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)
- 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)
- 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)
- 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)
- Avisek Das and Hans C. Andersen "The multiscale coarse-graining method. V. Isothermal-isobaric ensemble", Journal of Chemical Physics 132 164106 (2010)
- 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)
- Joseph F. Rudzinski and W. G. Noid "Coarse-graining entropy, forces, and structures", Journal of Chemical Physics 135 214101 (2011)
- 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)
- 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)