The Kabsch algorithm is an algorithm for computing the optimal rigid body transformation for aligning two sets of paired points. This post covers its implementation in NumPy, PyTorch, TensorFlow, and JAX.
This post explores the simulation of Pt adatom diffusion on a Pt(100) surface using LAMMPS, suggesting its potential as a simple toy model for machine learning applications, updating the previous Cu adatom diffusion simulation.
This post explores the simulation of Cu adatom diffusion on a Cu(100) surface using LAMMPS, suggesting its potential as a simple toy model for machine learning applications.
This repository contains scripts for generating trajectories of mini proteins using GROMACS. Mini proteins are small proteins with only a few amino acids, and they are frequently used as test cases for new methods in molecular dynamics, from new force fields to new sampling algorithms. This repository contains scripts for generating trajectories of mini proteins, including alanine dipeptide, glycine dipeptide, isoleucine dipeptide, leucine dipeptide, methionine dipeptide, phenylalanine dipeptide, proline dipeptide, tryptophan dipeptide, and valine dipeptide.