Notebook-integrated tools for molecular simulation and visualization

A collection of interactive notebooks to explain concepts of quantum mechanics and related topics

Google Colab notebooks for running molecular dynamics simulations with GROMACS

IPython API to visualize MD-trajectories along projected trajectories inside a Jupyter notebook

Open Source, Mostly just clicking mouse to finish a simulation with Ambertools and OpenMM. It was designed to use locally but another notebook to finish the simulaiton on Colab was attached as well.

A repository providing jupyter notebooks and simulation inputs that accompany the mini course Hands-on tutorials: Advanced sampling methods using GROMACS

A tutorial demonstrating the use of machine learning for the classification of crystal structures in a molecular dynamics simulation.

📓 Overview the OpenMM Molecular Dynamics Engine

CAMSAI Notebooks provides interactive Jupyter notebooks for AI-driven materials science research. These notebooks demonstrate the use of CAMSAI tools, schemas, and workflows, offering hands-on examples for data validation, materials design, and AI integration to accelerate scientific discovery.

Jupyter notebooks used for retraining the ReaxFF force field for the inorganic compound LiF.

Data analysis scripts and notebooks for interfacial polyelectrolyte molecular dynamics simulations using Gromacs.

Building single crystal structures easily

Google colab notebooks for typical MD trajectory analysis routines with Python

Github repo for the submission of the codes and notebooks for the LSN course at UNIMI

Example workflows using the flowws library

Python/Jupyter Notebook code that utilizes the NetworkX package to locate cyclic structures within an MD simulation

This notebook shows how to use variance constrained semi grand canonical (VC-SGC) Molecular Dynamics/Monte Carlo (MD/MC) calculations in pyiron

This is a repository for the class PHYS-7810: Computational Statistical Physics at CU Boulder that includes jupyter notebooks of tutorials and homework.

This project demonstrates how atomistic simulations are used to predict and analyze the behavior of atoms and molecules, providing detailed tutorials and simulations in a Jupyter Notebook.

This is a Jupyter Notebook to illustrate the difference between the Velocity-Verlet and Euler methods for integrating classical equations of motion for a homonuclear diatomic molecule.