Coarse graining

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 , 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

• Multi-particle collision dynamics

References

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)
• 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)
• 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)