Molecular Dynamics Python Packages

mdanalysis

MDAnalysis is a Python library to analyze molecular dynamics simulations.

nequip

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

nequip-allegro

Allegro is an open-source code for building highly scalable and accurate equivariant deep learning interatomic potentials

freud-analysis

Powerful, efficient particle trajectory analysis in scientific Python.

packmol

Packmol - Initial configurations for molecular dynamics simulations

mdapy

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

alchemlyb

the simple alchemistry library

prolif

Interaction Fingerprints for protein-ligand complexes and more

alchemtest

the simple alchemistry test set

deepmd-kit

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

kinisi

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

physical-validation

Physical validation of molecular simulations

metatrain

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

pyztraj

High-performance molecular dynamics trajectory analysis library in Zig

pymolar

Repository for molar crate and its dependencies

zsasa

High-performance SASA (Solvent Accessible Surface Area) calculation in Zig with Python bindings

upet

Universal interatomic potentials for advanced materials modeling

znh5md

ZnH5MD - High Performance Interface for H5MD Trajectories

dynaphopy

Phonon anharmonicity analysis from molecular dynamics

moltemplate

A general cross-platform text-based molecule builder for LAMMPS

inductiva

Large scale simulations made simple.

mdanalysistests

MDAnalysis is a Python library to analyze molecular dynamics simulations.

gromacswrapper

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

vermouth

Describe and apply transformation on molecular structures and topologies