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

prolif

Interaction Fingerprints for protein-ligand complexes and more

freud-analysis

Powerful, efficient particle trajectory analysis in scientific Python.

alchemlyb

the simple alchemistry library

packmol

Packmol - Initial configurations for molecular dynamics simulations

hbat

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

mdapy

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

alchemtest

the simple alchemistry test set

metatrain

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

kinisi

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

zsasa

Fast SASA calculation using Zig

deepmd-kit

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

upet

Universal interatomic potentials for advanced materials modeling

znh5md

ZnH5MD - High Performance Interface for H5MD Trajectories

physical-validation

Physical validation of molecular simulations

pyztraj

High-performance molecular dynamics trajectory analysis library in Zig

mdanalysistests

MDAnalysis is a Python library to analyze molecular dynamics simulations.

pymolar

Repository for molar crate and its dependencies

kliff

KIM-based Learning-Integrated Fitting Framework for interatomic potentials.

alphadynamics

Compact sequence-only neural propagator for protein torsion dynamics. 2.39x lower JSD than Microsoft Timewarp at 3000x fewer parameters. pip install alphadynamics.

moltemplate

A general cross-platform tool for preparing simulations of molecules and complex molecular assemblies

gromacswrapper

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