Molecular Dynamics Python Packages

mdanalysis

MDAnalysis is a Python library to analyze molecular dynamics simulations.

prolif

Interaction Fingerprints for protein-ligand complexes and more

alchemlyb

the simple alchemistry library

packmol

Packmol - Initial configurations for molecular dynamics simulations

metatrain

Train, fine-tune, and manipulate machine learning models for atomistic systems

nequip

NequIP is a code for building E(3)-equivariant interatomic potentials

hbat

HBAT 2: A Python Package to analyse Hydrogen Bonds and Other Non-covalent Interactions in Macromolecular Structures

freud-analysis

Powerful, efficient particle trajectory analysis in scientific Python.

upet

Universal machine-learning models for advanced atomistic simulations

alchemtest

the simple alchemistry test set

kinisi

A Python package for estimating diffusion properties from molecular dynamics simulations.

nequip-allegro

Allegro is a code for building highly scalable E(3)-equivariant interatomic potentials

deepmd-kit

A deep learning package for many-body potential energy representation and molecular dynamics

physical-validation

Physical validation of molecular simulations

mdanalysistests

MDAnalysis is a Python library to analyze molecular dynamics simulations.

synth-pdb

Generate realistic PDB files with mixed secondary structures for testing, education and bioinformatics tool development. Jupyter Notebook tutorials are available to visualize the concepts..

mdanalysisdata

Access to data for workshops and extended tests of MDAnalysis.

mdapy

A simple and fast python library to handle the data generated from molecular dynamics simulations

vermouth

Describe and apply transformation on molecular structures and topologies

torch-pme

Particle-mesh based calculations of long-range interactions in PyTorch

molcrafts-molpy-nightly

A fast, clean, and composable toolkit for molecular modeling

inductiva

Large scale simulations made simple.

dynaphopy

Phonon anharmonicity analysis from molecular dynamics

gromacswrapper

GromacsWrapper wraps system calls to GROMACS tools into thin Python classes (GROMACS 4.6.5 - 2024 supported).