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 …

Statistically optimal force aggregation for coarse-graining molecular dynamics

A Krämer, AEP Durumeric, NE Charron… - The Journal of …, 2023 - ACS Publications
Machine-learned coarse-grained (CG) models have the potential for simulating large
molecular complexes beyond what is possible with atomistic molecular dynamics. However …

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 …

[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 …

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 …

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 …

Deep coarse-grained potentials via relative entropy minimization

S Thaler, M Stupp, J Zavadlav - The Journal of Chemical Physics, 2022 - pubs.aip.org
Neural network (NN) potentials are a natural choice for coarse-grained (CG) models. Their
many-body capacity allows highly accurate approximations of the potential of mean force …

Neural network based prediction of conformational free energies-a new route toward coarse-grained simulation models

T Lemke, C Peter - Journal of chemical theory and computation, 2017 - ACS Publications
Coarse-grained (CG) simulation models have become very popular tools to study complex
molecular systems with great computational efficiency on length and time scales that are …

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 …