The multiscale coarse-graining method. I. A rigorous bridge between atomistic and coarse-grained models
Coarse-grained (CG) models provide a computationally efficient method for rapidly
investigating the long time-and length-scale processes that play a critical role in many …
investigating the long time-and length-scale processes that play a critical role in many …
The multiscale coarse-graining method. II. Numerical implementation for coarse-grained molecular models
The multiscale coarse-graining (MS-CG) method [S. Izvekov and GA Voth, J. Phys. Chem. B
109, 2469 (2005); J. Chem. Phys. 123, 134105 (2005)] employs a variational principle to …
109, 2469 (2005); J. Chem. Phys. 123, 134105 (2005)] employs a variational principle to …
Coarse-graining entropy, forces, and structures
JF Rudzinski, WG Noid - The Journal of chemical physics, 2011 - pubs.aip.org
Coarse-grained (CG) models enable highly efficient simulations of complex processes that
cannot be effectively studied with more detailed models. CG models are often parameterized …
cannot be effectively studied with more detailed models. CG models are often parameterized …
The multiscale coarse-graining method. V. Isothermal-isobaric ensemble
A Das, HC Andersen - The Journal of chemical physics, 2010 - pubs.aip.org
The multiscale coarse-graining (MS-CG) method is a method for determining the effective
potential energy function for a coarse-grained (CG) model of a system using the data …
potential energy function for a coarse-grained (CG) model of a system using the data …
OpenMSCG: A software tool for bottom-up coarse-graining
The “bottom-up” approach to coarse-graining, for building accurate and efficient
computational models to simulate large-scale and complex phenomena and processes, is …
computational models to simulate large-scale and complex phenomena and processes, is …
Multiscale coarse-graining and structural correlations: Connections to liquid-state theory
A statistical mechanical framework elucidates the significance of structural correlations
between coarse-grained (CG) sites in the multiscale coarse-graining (MS-CG) method …
between coarse-grained (CG) sites in the multiscale coarse-graining (MS-CG) method …
Systematic methods for structurally consistent coarse-grained models
WG Noid - Biomolecular Simulations: Methods and Protocols, 2013 - Springer
This chapter provides a primer on theories for coarse-grained (CG) modeling and, in
particular, reviews several systematic methods for determining effective potentials for CG …
particular, reviews several systematic methods for determining effective potentials for CG …
Bottom-up coarse-graining: Principles and perspectives
Large-scale computational molecular models provide scientists a means to investigate the
effect of microscopic details on emergent mesoscopic behavior. Elucidating the relationship …
effect of microscopic details on emergent mesoscopic behavior. Elucidating the relationship …
The theory of ultra-coarse-graining. 1. General principles
Coarse-grained (CG) models provide a computationally efficient means to study
biomolecular and other soft matter processes involving large numbers of atoms correlated …
biomolecular and other soft matter processes involving large numbers of atoms correlated …
Efficient, regularized, and scalable algorithms for multiscale coarse-graining
L Lu, S Izvekov, A Das, HC Andersen… - Journal of chemical …, 2010 - ACS Publications
The multiscale coarse-graining (MS-CG) method obtains CG interactions from atomistic
configurations, as demonstrated previously for a variety of soft matter and biological …
configurations, as demonstrated previously for a variety of soft matter and biological …