All-Atom Molecular Dynamics
Retaining full atomic resolution without electronic structure calculations, this method describes interactions at the atomic level to capture both static distributions and dynamic properties of atoms and molecules
Overview
All-atom molecular dynamics tracks every atom in a system, including every water molecule, every ion, and every bond, and calculates how they move under physical forces: bonding interactions, electrical attractions and repulsions, and weak van der Waals attractions. Unlike coarse-grained simulations that group atoms into simplified beads, all-atom models preserve the full molecular detail needed to resolve phenomena such as local structural heterogeneity in supercooled liquids, the kinetics of polymer ordering, and the step-by-step mechanism of ion dissolution in water.
Current Focus
Active microrheology of glasses: Pulling a single nanoscale probe through a model metallic glass and measuring the friction force it encounters. This friction encodes the glass transition and reveals local mechanical differences within the material that bulk measurements cannot see
Block copolymer ordering pathways: Following how a disordered polymer melt organizes into hexagonally packed cylinders, including transient intermediate states where cylinders have formed but not yet aligned
Ion dissolution mechanisms: Tracking how water molecules cooperatively enter the coordination shell of dissolving metal ions such as Al³⁺, revealing that the sequence and geometry of approach determine the dissolution pathway
Atomistic validation of coarse-grained models: Providing reference structural and dynamical measurements from all-atom trajectories as calibration targets for the lab's simplified coarse-grained models
Methods
The interactive visualizations on this page use an explicit-solvent trajectory of caffeine dissolved in water to illustrate core all-atom MD concepts: how atoms are represented, what force-field terms look like in practice, how local molecular structure varies from place to place, and how periodic boundary conditions work. The trajectory is one example; these concepts apply to any all-atom simulation of a liquid or solution.
Related Publications
Yu et al., Science Advances (2020), Active microrheology of metallic glass
Madanchi et al., Soft Matter (2021), Friction dynamics in glass
Seo et al., Soft Matter (2020), Cylindrical microphase separation
Kim et al., J. Phys. Chem. Lett. (2024), Al³⁺ dissolution