Machine learning of coarse-grained molecular dynamics force fields

J Wang, S Olsson, C Wehmeyer, A Pérez… - ACS central …, 2019 - ACS Publications
Atomistic or ab initio molecular dynamics simulations are widely used to predict
thermodynamics and kinetics and relate them to molecular structure. A common approach to …

Flow-matching: Efficient coarse-graining of molecular dynamics without forces

J Kohler, Y Chen, A Kramer, C Clementi… - Journal of Chemical …, 2023 - ACS Publications
Coarse-grained (CG) molecular simulations have become a standard tool to study molecular
processes on time and length scales inaccessible to all-atom simulations. Parametrizing CG …

Coarse-graining with equivariant neural networks: A path toward accurate and data-efficient models

TD Loose, PG Sahrmann, TS Qu… - The Journal of Physical …, 2023 - ACS Publications
Machine learning has recently entered into the mainstream of coarse-grained (CG)
molecular modeling and simulation. While a variety of methods for incorporating deep …

[HTML][HTML] Coarse graining molecular dynamics with graph neural networks

BE Husic, NE Charron, D Lemm, J Wang… - The Journal of …, 2020 - pubs.aip.org
Coarse graining enables the investigation of molecular dynamics for larger systems and at
longer timescales than is possible at an atomic resolution. However, a coarse graining …

Machine learned coarse-grained protein force-fields: Are we there yet?

AEP Durumeric, NE Charron, C Templeton… - Current opinion in …, 2023 - Elsevier
The successful recent application of machine learning methods to scientific problems
includes the learning of flexible and accurate atomic-level force-fields for materials and …

Two for one: Diffusion models and force fields for coarse-grained molecular dynamics

M Arts, V Garcia Satorras, CW Huang… - Journal of Chemical …, 2023 - ACS Publications
Coarse-grained (CG) molecular dynamics enables the study of biological processes at
temporal and spatial scales that would be intractable at an atomistic resolution. 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 …

[HTML][HTML] Coarse-graining auto-encoders for molecular dynamics

W Wang, R Gómez-Bombarelli - npj Computational Materials, 2019 - nature.com
Molecular dynamics simulations provide theoretical insight into the microscopic behavior of
condensed-phase materials and, as a predictive tool, enable computational design of new …

Ensuring thermodynamic consistency with invertible coarse-graining

S Chennakesavalu, DJ Toomer… - The Journal of Chemical …, 2023 - pubs.aip.org
Coarse-grained models are a core computational tool in theoretical chemistry and
biophysics. A judicious choice of a coarse-grained model can yield physical insights by …

Coarse-graining errors and numerical optimization using a relative entropy framework

A Chaimovich, MS Shell - The Journal of chemical physics, 2011 - pubs.aip.org
The ability to generate accurate coarse-grained models from reference fully atomic (or
otherwise “first-principles”) ones has become an important component in modeling the …