Highly scalable and memory efficient ultra-coarse-grained molecular dynamics simulations

JMA Grime, GA Voth - Journal of chemical theory and computation, 2014 - ACS Publications
The use of coarse-grained (CG) models can significantly increase the time and length scales
accessible to computational molecular dynamics (MD) simulations. To address very large …

A review of coarse-grained molecular dynamics techniques to access extended spatial and temporal scales in biomolecular simulations

BA Merchant, JD Madura - Annual Reports in Computational Chemistry, 2011 - Elsevier
The study of very large biomolecular systems over extended spatial and temporal scales is
being accomplished through the use of coarse-grained (CG) models. The successes of …

[HTML][HTML] Introduction: Coarse-graining in molecular modeling and simulation

GA Voth - Journal of Chemical Theory and Computation, 2006 - ACS Publications
This partial special issue of the Journal of Chemical Theory and Computation is devoted to
the topic of coarsegraining in molecular modeling and simulation. To my knowledge, it is the …

Enhanced Sampling of an Atomic Model with Hybrid Nonequilibrium Molecular Dynamics Monte Carlo Simulations Guided by a Coarse-Grained Model

Y Chen, B Roux - Journal of Chemical Theory and Computation, 2015 - ACS Publications
Molecular dynamics (MD) trajectories based on a classical equation of motion provide a
straightforward, albeit somewhat inefficient approach, to explore and sample the …

A test of systematic coarse-graining of molecular dynamics simulations: Thermodynamic properties

CC Fu, PM Kulkarni, M Scott Shell… - The Journal of Chemical …, 2012 - pubs.aip.org
Coarse-graining (CG) techniques have recently attracted great interest for providing
descriptions at a mesoscopic level of resolution that preserve fluid thermodynamic and …

[HTML][HTML] Encoding and selecting coarse-grain mapping operators with hierarchical graphs

M Chakraborty, C Xu, AD White - The Journal of Chemical Physics, 2018 - pubs.aip.org
Coarse-grained (CG) molecular dynamics (MD) can simulate systems inaccessible to fine-
grained (FG) MD simulations. A CG simulation decreases the degrees of freedom by …

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 …

[HTML][HTML] Magic v. 3: An integrated software package for systematic structure-based coarse-graining

A Mirzoev, L Nordenskiöld, A Lyubartsev - Computer Physics …, 2019 - Elsevier
Molecular simulations of many phenomena related to biomolecular systems, soft matter and
nanomaterials require consideration of length scales above 10 nm and time scales longer …

Modeling real dynamics in the coarse-grained representation of condensed phase systems

S Izvekov, GA Voth - The Journal of chemical physics, 2006 - pubs.aip.org
This work presents a systematic multiscale methodology to provide a more faithful
representation of real dynamics in coarse-grained molecular simulation models. The …

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 …