Notebook-integrated tools for molecular simulation and visualization
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Updated
Apr 2, 2018 - Python
Molecular dynamics allows the atoms and molecules to interact for a fixed period of time, giving a view of the dynamic "evolution" of the system.
Notebook-integrated tools for molecular simulation and visualization
IPython API to visualize MD-trajectories along projected trajectories inside a Jupyter notebook
📓 Overview the OpenMM Molecular Dynamics Engine
A tutorial demonstrating the use of machine learning for the classification of crystal structures in a molecular dynamics simulation.
Example workflows using the flowws library
This notebook shows how to use variance constrained semi grand canonical (VC-SGC) Molecular Dynamics/Monte Carlo (MD/MC) calculations in pyiron
Building single crystal structures easily
A repository providing jupyter notebooks and simulation inputs that accompany the mini course Hands-on tutorials: Advanced sampling methods using GROMACS
Python/Jupyter Notebook code that utilizes the NetworkX package to locate cyclic structures within an MD simulation
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.
Google colab notebooks for typical MD trajectory analysis routines with Python
Google Colab notebooks for running molecular dynamics simulations with GROMACS
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.
Github repo for the submission of the codes and notebooks for the LSN course at UNIMI
Jupyter notebooks used for retraining the ReaxFF force field for the inorganic compound LiF.
A collection of interactive notebooks to explain concepts of quantum mechanics and related topics