Müller-Brown Basin MA: Langevin Dynamics Simulation
Langevin dynamics simulation showing particle motion in the deep reactant minimum (Basin MA) of the Müller-Brown …
Simulation
Müller-Brown Basin MB: Langevin Dynamics Simulation
Langevin dynamics simulation showing particle motion in the product minimum (Basin MB) of the Müller-Brown potential …
Müller-Brown Transition: Langevin Dynamics Simulation
Extended Langevin dynamics simulation showing particle transitions between different basins of the Müller-Brown …
Liquid Argon: LAMMPS Simulation
LAMMPS molecular dynamics simulation of liquid argon demonstrating fundamental liquid-state behavior and molecular …
Rahman's 1964 Liquid Argon Simulation Replication
Replication of Rahman's 1964 molecular dynamics simulation using modern LAMMPS and Python, achieving quantitative …...
Replicating Rahman's 1964 Liquid Argon Simulation
Recreating the foundational 1964 molecular dynamics simulation with modern Python and LAMMPS, testing whether Rahman's …...
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 …
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 …
Mini-Protein Trajectory Generation
GROMACS workflows for amino acid dipeptide trajectories across nine residue types, creating diverse MD datasets for ML …