buildH
buildH: Build hydrogen atoms from united-atom molecular dynamics of lipids and calculate the order parameters - Published in JOSS (2021)
Project RACCOON
Project RACCOON: Automated construction of PDB files for polymers and polymer peptide conjugates - Published in JOSS (2024)
FlowerMD
FlowerMD: Flexible Library of Organic Workflows and Extensible Recipes for Molecular Dynamics - Published in JOSS (2023)
polypy - Analysis Tools for Solid State Molecular Dynamics and Monte Carlo Trajectories
polypy - Analysis Tools for Solid State Molecular Dynamics and Monte Carlo Trajectories - Published in JOSS (2021)
mdanalysis
MDAnalysis is a Python library to analyze molecular dynamics simulations.
openpathsampling
An open source Python framework for transition interface and path sampling calculations.
https://github.com/kevinshen56714/emc-pypi
Python interface for Enhanced Monte Carlo (EMC)
https://github.com/becksteinlab/propkatraj
pKa estimates for proteins using an ensemble approach
https://github.com/theochem/iodata
Python library for reading, writing, and converting computational chemistry file formats and generating input files.
https://github.com/yesint/molar
Repository for molar crate and its dependencies
pychastic
Pychastic is a stochastic differential equations integrator written entirely in python.
rcbs.py
RCBS.py (Reactivity of Chemical and Biochemical Systems) is a Python package that contains several scripts, functions and classes that simplify the analysis of chemical and biochemical simulations.
https://github.com/m3g/complexmixtures.jl
Package to perform minimum-distance distribution analyses of complex solute-solvent interactions
https://github.com/radonpy/radonpy
RadonPy is a Python library to automate physical property calculations for polymer informatics.
NBodySimulator
A differentiable simulator for scientific machine learning (SciML) with N-body problems, including astrophysical and molecular dynamics
https://github.com/becksteinlab/mdanalysis-with-dask
Benchmarking MDAnalysis with dask.
https://github.com/arm61/falass
Neutron and X-ray Reflectometry from Computer Simulation
rotamerconvolvemd
Analysis of molecular dynamics trajectories or conformational ensembles in terms of spin-label distances as probed in double electron-electron resonance (DEER) experiments.
https://github.com/choderalab/yank
An open, extensible Python framework for GPU-accelerated alchemical free energy calculations.
https://github.com/becksteinlab/adkgromacstutorial
Basic tutorial for running and analyzing a Gromacs MD simulation of AdK
https://github.com/choderalab/ensembler
Automated omics-scale protein modeling and simulation setup.
hbondauto
HBondAuto is a program developed to calculate and automate the hydrogen bond analysis in Molecular Dynamics Simulations.
ls1-mardyn
ls1-MarDyn is a massively parallel Molecular Dynamics (MD) code for large systems. Its main target is the simulation of thermodynamics and nanofluidics. ls1-MarDyn is designed with a focus on performance and easy extensibility.
safep
Tools for Analyzing and Debugging (SA)FEP calculations. See also the SAFEP Tutorial: https://github.com/jhenin/SAFEP_tutorial/tree/main Documentation: https://safep-alchemy.readthedocs.io/en/latest/
amep
The Active Matter Evaluation Package (AMEP) - a Python library for the analysis of particle-based and continuum simulation data of soft and active matter systems
mdakit_sasa
Toolkit to calculate the surface accessible area of a molecular dynamic trajectory
easymda
Python package for easy analysis of MD simulations based on MDAnalysis.
hpc_submit_scripts
Slurm job scripts to run and analyze molecular dynamics simulations on high performance computers
mdtools
Scripts to prepare and analyze molecular dynamics simulations
asyncmd
asyncmd: A python library to orchestrate complex molecular dynamics simulation campaigns on high performance computing systems - Published in JOSS (2025)
https://github.com/HouGroup/mdgo
A codebase for classical molecular dynamics (MD) simulation setup and results analysis.
CellLists
Julia language implementation of the Cell Lists algorithm to solve the fixed-radius near neighbors problem including serial and multithreaded algorithms.
https://github.com/akohlmey/lammps-gui
LAMMPS-GUI - The graphical interface for learning and running LAMMPS
