Learning Smooth and Expressive Interatomic Potentials for Physical Property Prediction
Fu et al. propose energy conservation as a key MLIP diagnostic and introduce eSEN, bridging test accuracy and real …...
Materials
Liquid Argon: LAMMPS Simulation
LAMMPS molecular dynamics simulation of liquid argon demonstrating fundamental liquid-state behavior and molecular …
Replicating Rahman's 1964 Liquid Argon Simulation
Recreating the foundational 1964 molecular dynamics simulation with modern Python and LAMMPS, testing whether Rahman's …...
Embedded-atom method: Derivation and application to impurities, surfaces, and other defects in metals
Daw and Baskes's foundational 1984 paper introducing the Embedded-Atom Method (EAM), a many-body potential for metal …...
Processes of Adsorption and Diffusion on Solid Surfaces
Lennard-Jones's 1932 foundational paper introducing potential energy surface models to unify physical and chemical …...
GEOM Dataset: 3D Molecular Conformer Generation
Learn how GEOM transforms 2D molecular graphs into dynamic 3D conformer ensembles for molecular machine learning …
Kabsch Algorithm: NumPy, PyTorch, TensorFlow, and JAX
Learn about the Kabsch algorithm for optimal point alignment with implementations in NumPy, PyTorch, TensorFlow, and JAX …
Copper Adatom Diffusion on Cu(100): LAMMPS Simulation
LAMMPS molecular dynamics simulation of copper adatom diffusion on a Cu(100) surface, showing atomic mobility …
LAMMPS Tutorial: Copper Adatom Diffusion
LAMMPS tutorial for copper surface diffusion simulation and ML training data generation. Includes setup, analysis, and …
Platinum Adatom Diffusion on Pt(100) Surface
LAMMPS tutorial for platinum adatom diffusion simulation and ML training data. Learn how heavier atoms behave …
Platinum Adatom Diffusion on Pt(100): LAMMPS Simulation
LAMMPS molecular dynamics simulation of platinum adatom diffusion on a Pt(100) surface, showing atomic mobility …
Generating Mini-Protein Trajectories with GROMACS
Systematic GROMACS workflows for simulating mini-proteins across multiple amino acids to generate diverse MD …