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 …
molecular modeling and simulation. While a variety of methods for incorporating deep …
Statistically optimal force aggregation for coarse-graining molecular dynamics
Machine-learned coarse-grained (CG) models have the potential for simulating large
molecular complexes beyond what is possible with atomistic molecular dynamics. However …
molecular complexes beyond what is possible with atomistic molecular dynamics. However …
Machine learning of coarse-grained molecular dynamics force fields
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 …
thermodynamics and kinetics and relate them to molecular structure. A common approach to …
Flow-matching: Efficient coarse-graining of molecular dynamics without forces
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 …
processes on time and length scales inaccessible to all-atom simulations. Parametrizing CG …
[HTML][HTML] Coarse graining molecular dynamics with graph neural networks
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 …
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 …
large and complex systems in an efficient and inexpensive manner due to its lowered …
Bottom-up coarse-graining: Principles and perspectives
Large-scale computational molecular models provide scientists a means to investigate the
effect of microscopic details on emergent mesoscopic behavior. Elucidating the relationship …
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 …
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
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 …
molecular systems with great computational efficiency on length and time scales that are …
Machine learned coarse-grained protein force-fields: Are we there yet?
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 …
includes the learning of flexible and accurate atomic-level force-fields for materials and …