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 …

Perspective: Advances, challenges, and insight for predictive coarse-grained models

WG Noid - The Journal of Physical Chemistry B, 2023 - ACS Publications
By averaging over atomic details, coarse-grained (CG) models provide profound
computational and conceptual advantages for studying soft materials. In particular, bottom …

A review of advancements in coarse-grained molecular dynamics simulations

SY Joshi, SA Deshmukh - Molecular Simulation, 2021 - Taylor & Francis
Over the last few years, coarse-grained molecular dynamics has emerged as a way to model
large and complex systems in an efficient and inexpensive manner due to its lowered …

Chemically specific coarse‐graining of polymers: Methods and prospects

S Dhamankar, MA Webb - Journal of Polymer Science, 2021 - Wiley Online Library
Coarse‐grained (CG) modeling is an invaluable tool for the study of polymers and other soft
matter systems due to the span of spatiotemporal scales that typify their physics and …

Perspective: Coarse-grained models for biomolecular systems

WG Noid - The Journal of chemical physics, 2013 - pubs.aip.org
By focusing on essential features, while averaging over less important details, coarse-
grained (CG) models provide significant computational and conceptual advantages with …

GROMACS 4: algorithms for highly efficient, load-balanced, and scalable molecular simulation

B Hess, C Kutzner, D Van Der Spoel… - Journal of chemical …, 2008 - ACS Publications
Molecular simulation is an extremely useful, but computationally very expensive tool for
studies of chemical and biomolecular systems. Here, we present a new implementation of …

Introducing memory in coarse-grained molecular simulations

V Klippenstein, M Tripathy, G Jung… - The Journal of …, 2021 - ACS Publications
Preserving the correct dynamics at the coarse-grained (CG) level is a pressing problem in
the development of systematic CG models in soft matter simulation. Starting from the seminal …

Systematic coarse-graining methods for soft matter simulations–a review

E Brini, EA Algaer, P Ganguly, C Li… - Soft Matter, 2013 - pubs.rsc.org
Multiscale modelling of soft matter is an emerging field that has made rapid progress in the
past decade. Several methods for systematic coarse-graining of molecular liquids and soft …

Versatile object-oriented toolkit for coarse-graining applications

V Ruhle, C Junghans, A Lukyanov… - Journal of chemical …, 2009 - ACS Publications
Coarse-graining is a systematic way of reducing the number of degrees of freedom
representing a system of interest. Several coarse-graining techniques have so far been …

[图书][B] Coarse-graining of condensed phase and biomolecular systems

GA Voth - 2008 - taylorfrancis.com
Exploring recent developments in the field, Coarse-Graining of Condensed Phase and
Biomolecular Systems examines systematic ways of constructing coarse-grained …