[HTML][HTML] Coarse-graining involving virtual sites: Centers of symmetry coarse-graining

J Jin, Y Han, GA Voth - The Journal of Chemical Physics, 2019 - pubs.aip.org
Coarse-grained (CG) models allow efficient molecular simulation by reducing the degrees of
freedom in the system. To recapitulate important physical properties, including many-body …

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 …

[HTML][HTML] The impact of resolution upon entropy and information in coarse-grained models

TT Foley, MS Shell, WG Noid - The Journal of chemical physics, 2015 - pubs.aip.org
By eliminating unnecessary degrees of freedom, coarse-grained (CG) models tremendously
facilitate numerical calculations and theoretical analyses of complex phenomena. However …

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 …

Temperature and phase transferable bottom-up coarse-grained models

J Jin, A Yu, GA Voth - Journal of chemical theory and computation, 2020 - ACS Publications
Despite the high fidelity of bottom-up coarse-grained (CG) approaches to recapitulate the
structural correlations in atomistic simulations, the general use of bottom-up CG methods is …

Understanding missing entropy in coarse-grained systems: Addressing issues of representability and transferability

J Jin, AJ Pak, GA Voth - The journal of physical chemistry letters, 2019 - ACS Publications
Coarse-grained (CG) models facilitate efficient simulation of complex systems by integrating
out the atomic, or fine-grained (FG), degrees of freedom. Systematically derived CG models …

Enhancing pressure consistency and transferability of structure-based coarse-graining

J Tang, T Kobayashi, H Zhang, K Fukuzawa… - Physical Chemistry …, 2023 - pubs.rsc.org
Coarse-graining, which models molecules with coarse-grained (CG) beads, allows
molecular dynamics simulations to be applied to systems with large length and time scales …

[HTML][HTML] A microcanonical approach to temperature-transferable coarse-grained models using the relative entropy

E Pretti, MS Shell - The Journal of Chemical Physics, 2021 - pubs.aip.org
Bottom-up coarse-graining methods provide systematic tools for creating simplified models
of molecular systems. However, coarse-grained (CG) models produced with such methods …

Statistical mechanical design principles for coarse-grained interactions across different conformational free energy surfaces

J Jin, GA Voth - The Journal of Physical Chemistry Letters, 2023 - ACS Publications
Systematic bottom-up coarse-graining (CG) of molecular systems provides a means to
explore different coupled length and time scales while treating the molecular-scale physics …

Analysis of mapping atomic models to coarse-grained resolution

KM Kidder, WG Noid - The Journal of Chemical Physics, 2024 - pubs.aip.org
Low-resolution coarse-grained (CG) models provide significant computational and
conceptual advantages for simulating soft materials. However, the properties of CG models …