Molecular Dynamics Simulation Python Packages

mdanalysis

MDAnalysis is a Python library to analyze molecular dynamics simulations.

hbat

HBAT 2: A Python Package to analyse Hydrogen Bonds and Other Non-covalent Interactions in Macromolecular Structures https://hbat-web.abhishek-tiwari.com

mdanalysistests

MDAnalysis is a Python library to analyze molecular dynamics simulations.

qc-iodata

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

gmx-clusterbyfeatures

Features Based Conformational Clustering of MD trajectories. See details at:

maicos

Analyse molecular dynamics simulations of interfacial and confined systems.

pymolar

Repository for molar crate and its dependencies

mdacli

Command line interface for MDAnalysis

mdadash

Dashboard for monitoring running MD simulations using streaming (GSoC 2026).

buildh

:computer: Build hydrogen atoms from united-atom molecular dynamics of lipids and calculate the order parameters.

pyadmd

Setup and run aMDeNM simulations with Python

radonpy-pypi

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

emc-pypi

Python interface for Enhanced Monte Carlo (EMC)

streamd

Fully automated high-throughput MD pipeline

amber-mlips

MLIP (Machine Learning Interatomic Potential) plugins for ML/MM MD simulations with AmberTools25.

asyncmd

asyncmd is a library to write concurrent code to run and analyze molecular dynamics simulations using pythons async/await syntax. Computationally costly operations can be performed locally or submitted to a queuing system.

q2m3

A Hybrid Quantum-Classical QM/MM Simulation Framework

waternetworkanalysis

Set of tools for input preparation for conserved water search from MD trajectories (gromacs, amber) and their analysis

openpathsampling

An open source Python framework for transition interface and path sampling calculations.

amep

Python data analysis package for active and soft matter simulations

biofilmsimulation

This repository contains the code for simulating the growth of a Biofilm after attachment using Molecular dynamics simulation methods. The project was build as part of the iGEM 2020 Contest. The BiofilmSimulation software can be installed as A python package, documented under https://pypi.org/project/BiofilmSimulation.

membrane-curvature

MDAnalysis tool to calculate membrane curvature.

metadynminer

Python package for efficient analysis of HILLS files generated by Plumed metadynamics simulations. Inspired by the Metadynminer package for R.

lazydock

LazyDock: Lazy Dock, Easy Life