Umbrella Sampling: Monte Carlo Free-Energy Estimation
Torrie and Valleau's 1977 paper introducing Umbrella Sampling, an importance sampling technique for Monte Carlo …
Molecular-Dynamics - Page 3
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 and Platinum Adatom Diffusion
LAMMPS tutorial for copper and platinum surface diffusion simulation and ML training data generation. Includes setup, …
Platinum Adatom Diffusion on Pt(100): LAMMPS Simulation
LAMMPS molecular dynamics simulation of platinum adatom diffusion on a Pt(100) surface, showing atomic mobility …
Automated Adatom Diffusion Workflow
Python-wrapped reference implementation for surface diffusion simulations using LAMMPS and EAM potentials, with …
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
Automated GROMACS pipeline generating high-fidelity MD trajectories with atomic force extraction for Neural Network …