Coarse-Graining Auto-Encoders for Molecular Dynamics

Understand

Molecular dynamics simulations provide theoretical insight into the microscopic behavior of materials in condensed phase and, as a predictive tool, enable computational design of new compounds.

• However, because of the large temporal and spatial scales involved in thermodynamic and kinetic phenomena in materials, atomistic simulations are often computationally unfeasible.
• Coarse-graining methods allow simulating larger systems, by reducing the dimensionality of the simulation, and propagating longer timesteps, by averaging out fast motions.
• Coarse-graining involves two coupled learning problems; defining the mapping from an all-atom to a reduced representation, and the parametrization of a Hamiltonian over coarse-grained coordinates.