Alanine dipeptide OpenMM-Plumed test

An ASE-friendly implementation of the amorphous-to-crystalline (a2c) workflow.

pyCHARMM tutorial, documentation and examples. This repository contains materials originally from the pyCHARMM Workshop run at the University of Michigan by Charles Brooks' Group, June 20-24.

Contact map analysis for biomolecules; based on MDTraj

gmx_MMPBSA is a new tool based on AMBER's MMPBSA.py aiming to perform end-state free energy calculations with GROMACS files.

This Python library makes it easy to display images and videos in a notebook.

COBY (Coarse Grained System Builder) can be used to create coarse-grained systems in Martini 3

Scripts and inputs to perform simulations of organic crystals and peptide crystals using GROMACS.

My Python Examples

Packmol - Initial configurations for molecular dynamics simulations

Molecular dynamics simulations with an LLM agent

Exercism exercises in Python.

Interface to OpenMM for easy setup of molecular dynamic simulations of protein-ligand complexes

Simple protein-ligand complex simulation with OpenMM

Parameter/topology editor and molecular simulator

🦀 Small exercises to get you used to reading and writing Rust code!

Code Accompanying "Ensemble Docking for Intrinsically Disordered Proteins" by Anjali Dhar, Thomas R. Sisk and Paul Robustelli.

PyGWalker: Turn your pandas dataframe into an interactive UI for visual analysis

A command line application to launch molecular dynamics simulations with OpenMM

A collections of scripts for working molecular dynamics simulations

Files for the py tutorial located at https://emleddin.github.io/2020-06-05-py-tutorial/

Simple example of creating, training, and running a machine learning potential for molecular dynamics

Materials for 1-day intermediate workshop

Command line tool for organizing and curating molecular dynamics force field parameters

A Jupyter Notebook / Jupyter Lab extension allowing for tiling of cells for a customizable and flexible layout reducing white space.