The Dark Side of the Forces: Assessing Non-Conservative Force Models for Atomistic Machine Learning
Summary of Bigi et al.'s 2025 paper that critically evaluates the trend of using non-conservative force models in atomistic machine learning, …
Molecular-Dynamics
12 posts tagged with molecular-dynamics.
Learning Smooth and Expressive Interatomic Potentials for Physical Property Prediction
Summary of Fu et al.'s 2025 paper that bridges the gap between test-set accuracy and downstream task performance for MLIPs by proposing energy …
Liquid Argon: LAMMPS Simulation
LAMMPS molecular dynamics simulation showing liquid argon behavior.
Breathing Life into a Classic: A Modern Replication of Rahman's 1964 Liquid Argon Simulation
A deep dive into a Python-based replication of Aneesur Rahman's seminal 1964 paper, exploring the foundations of molecular dynamics with modern tools …
Embedded-atom method: Derivation and application to impurities, surfaces, and other defects in metals
Summary of Daw and Baskes's 1984 paper that introduces the Embedded-Atom Method (EAM), a semi-empirical, many-body potential that became a cornerstone …
Correlations in the Motion of Atoms in Liquid Argon
Summary of Aneesur Rahman's 1964 paper that effectively founded the field of molecular dynamics simulation by demonstrating its power to reveal the …
Kabsch Algorithm: NumPy, PyTorch, TensorFlow, and JAX
Learn about the Kabsch algorithm for optimal point alignment with implementations in NumPy, PyTorch, TensorFlow, and JAX for ML applications.
LAMMPS Simulation: Pt Adatom Diffusion on Pt(100) Surface
Build LAMMPS molecular dynamics simulations of platinum surface diffusion. Setup and analysis tutorial for generating trajectory data.
Copper Adatom Diffusion on Cu(100): LAMMPS Simulation
LAMMPS molecular dynamics simulation showing copper adatom diffusion on a Cu(100) surface.
Platinum Adatom Diffusion on Pt(100): LAMMPS Simulation
LAMMPS molecular dynamics simulation showing platinum adatom diffusion on a Pt(100) surface.
Simulating Cu Adatom Diffusion with LAMMPS
Learn LAMMPS molecular dynamics: simulate copper adatom diffusion on Cu(100) surfaces with setup guide and trajectory analysis.
Generating Mini-Protein Trajectories with GROMACS
Build GROMACS workflows for simulating mini-proteins across multiple amino acids. Generate diverse MD trajectories for machine learning.