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

mdanalysistests

MDAnalysis is a Python library to analyze molecular dynamics simulations.

gmx-clusterbyfeatures

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

mdacli

Command line interface for MDAnalysis

maicos

Analyse molecular dynamics simulations of interfacial and confined systems.

mdadash

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

pymolar

Repository for molar crate and its dependencies

qc-iodata

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

membrane-curvature

MDAnalysis tool to calculate membrane curvature.

openpathsampling

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

buildh

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

propkatraj

pKa estimates for proteins using an ensemble approach

radonpy-pypi

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

emc-pypi

Python interface for Enhanced Monte Carlo (EMC)

mda

:hammer: Analysis Tools for MD Simulations

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.

waternetworkanalysis

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

amep

Python data analysis package for active and soft matter simulations

metadynminer

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

fastmdx

Software for automated molecular dynamics exploration

dnamd

To analyze fluctuations in DNA or RNA structures in molecular dynamics trajectories.

fastmdanalysis

Software for automated molecular dynamics exploration

biofilmsimulation

The model applies methods from molecular dynamics (MD) and takes into account different physical and biological effects. The software provides great flexibility by enabling the user to switch easily between sets of constants e.g. to model different bacterial strains. Furthermore, the software includes functions for visualisation of the models behaviour over time.