The multiscale coarse-graining method. I. A rigorous bridge between atomistic and coarse-grained models

WG Noid, JW Chu, GS Ayton, V Krishna… - The Journal of …, 2008 - pubs.aip.org
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 …

The multiscale coarse-graining method. II. Numerical implementation for coarse-grained molecular models

WG Noid, P Liu, Y Wang, JW Chu, GS Ayton… - The Journal of …, 2008 - pubs.aip.org
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 …

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 …

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 …

OpenMSCG: A software tool for bottom-up coarse-graining

Y Peng, AJ Pak, AEP Durumeric… - The Journal of …, 2023 - ACS Publications
The “bottom-up” approach to coarse-graining, for building accurate and efficient
computational models to simulate large-scale and complex phenomena and processes, is …

Multiscale coarse-graining and structural correlations: Connections to liquid-state theory

WG Noid, JW Chu, GS Ayton… - The Journal of Physical …, 2007 - ACS Publications
A statistical mechanical framework elucidates the significance of structural correlations
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 …

Bottom-up coarse-graining: Principles and perspectives

J Jin, AJ Pak, AEP Durumeric, TD Loose… - Journal of chemical …, 2022 - ACS Publications
Large-scale computational molecular models provide scientists a means to investigate the
effect of microscopic details on emergent mesoscopic behavior. Elucidating the relationship …

The theory of ultra-coarse-graining. 1. General principles

JF Dama, AV Sinitskiy, M McCullagh… - Journal of chemical …, 2013 - ACS Publications
Coarse-grained (CG) models provide a computationally efficient means to study
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 …