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 …
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 …
Contrastive learning of coarse-grained force fields
Coarse-grained models have proven helpful for simulating complex systems over long time
scales to provide molecular insights into various processes. Methodologies for systematic …
scales to provide molecular insights into various processes. Methodologies for systematic …
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 …
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 …
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 …
[HTML][HTML] Multi-body effects in a coarse-grained protein force field
The use of coarse-grained (CG) models is a popular approach to study complex
biomolecular systems. By reducing the number of degrees of freedom, a CG model can …
biomolecular systems. By reducing the number of degrees of freedom, a CG model can …
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 …
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 …
A review of physics-based coarse-grained potentials for the simulations of protein structure and dynamics
By simplifying the atomistic representation of a biomolecular system, coarse-grained (CG)
approach enables the molecular dynamics simulation to reveal the biological processes …
approach enables the molecular dynamics simulation to reveal the biological processes …