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 …
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 …
[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 …
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 …
Two for one: Diffusion models and force fields for coarse-grained molecular dynamics
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 …
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 …
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 …
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 …
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 …
otherwise “first-principles”) ones has become an important component in modeling the …