Molecular Dynamics

Sample codes for my CUDA programming book

MDAnalysis is a Python library to analyze molecular dynamics simulations.

Graphics Processing Units Molecular Dynamics

Fortran and Python examples to accompany the book "Computer Simulation of Liquids" by Michael P. Allen and Dominic J. Tildesley (2nd edition, Oxford University Press, 2017). Use the "Code" button, or follow the "Releases" link below.

Sample codes for my book on molecular dynamics simulation

An open, extensible Python framework for GPU-accelerated alchemical free energy calculations.

RadonPy is a Python library to automate physical property calculations for polymer informatics.

Educational materials for, and related to, UC Irvine's Drug Discovery Computing Techniques course (PharmSci 175/275), currently taught by David Mobley.

Python library for reading, writing, and converting computational chemistry file formats and generating input files.

A differentiable simulator for scientific machine learning (SciML) with N-body problems, including astrophysical and molecular dynamics

Molecular dynamics simulation software

LAMMPS tutorials for both beginners and advanced users

Flexible implementation of cell lists to map the calculations of particle-pair dependent functions, such as forces, energies, neighbor lists, etc.

Monte Carlo and Molecular Dynamics Simulation Package

Geometric deep learning of protein–DNA binding specificity

A solar system simulator with Verlet, using OpenGL for displaying.

Real time molecular dynamics in the browser using LAMMPS

Automated omics-scale protein modeling and simulation setup.

MiniMD Molecular Dynamics Mini-App