Molecular Dynamics Python Packages

packmol

Packmol - Initial configurations for molecular dynamics simulations

mdtraj

An open library for the analysis of molecular dynamics trajectories

mdanalysis

MDAnalysis is a Python library to analyze molecular dynamics simulations.

readcon-db

Mmap CON campaign corpus (Heed/LMDB); companion to readcon-core under LODE

alchemlyb

the simple alchemistry library

prolif

Interaction Fingerprints for protein-ligand complexes and more

deepmd-kit

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

metatrain

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

physical-validation

Physical validation of molecular 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

upet

Universal machine-learning models for advanced atomistic simulations

mdapy

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

kinisi

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

freud-analysis

Powerful, efficient particle trajectory analysis in scientific Python.

mdanalysistests

MDAnalysis is a Python library to analyze molecular dynamics simulations.

nequip

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

vermouth

Describe and apply transformation on molecular structures and topologies

znh5md

ZnH5MD - High Performance Interface for H5MD Trajectories

qc-iodata

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

diffbio

End-to-end differentiable bioinformatics for JAX/Flax NNX: soft Smith-Waterman alignment, read mapping and assembly, variant calling, RNA-seq, single-cell, epigenomics, CRISPR, metabolomics, multi-omics, protein and RNA structure, molecular dynamics and drug-discovery operators composed into trainable pipelines on the Avitai stack.

dynaphopy

Phonon anharmonicity analysis from molecular dynamics

inductiva

Large scale simulations made simple.

molecularnodes

Toolbox for molecular animations in Blender, powered by Geometry Nodes.

gromacswrapper

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