Molecular Simulation Python Packages

mdanalysis

MDAnalysis is a Python library to analyze molecular dynamics simulations.

physical-validation

Physical validation of molecular simulations

moleculekit

MoleculeKit: Your favorite molecule manipulation kit

mdanalysistests

MDAnalysis is a Python library to analyze molecular dynamics simulations.

torchani

TorchANI 2.0 is an open-source library that supports training, development, and research of ANI-style neural network interatomic potentials. It was originally developed and is currently maintained by the Roitberg group.

spindry

Low-cost host-guest conformer generation

mchammer

Implementation of cheap Monte Carlo optimisation of bonds in molecules

qc-iodata

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

westpa

WESTPA: The Weighted Ensemble Simulation Toolkit with Parallelization and Analysis

quantumtuna

A streamlined quantum chemistry program for atoms and diatomics.

molarverse-pqsetup

Prepare and validate PQ simulation inputs.

mbuild

A hierarchical, component based molecule builder

foyer

A package for atom-typing as well as applying and disseminating forcefields

cgexplore

A general tool set for working with coarse-grained stk models

adaptivepele

AdaptivePELE is a Python package aimed at enhancing the sampling of molecular simulations

deerpredict

Software for the prediction of DEER and PRE data from conformational ensembles.

rcbs-py

RCBS.py (Reactivity of Chemical and Biochemical Systems) is a Python package that contains several scripts, functions and classes that simplify the analysis of chemical and biochemical simulations.

iodata

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

mbgdml

Create, use, and analyze machine learning potentials within the many-body expansion framework.

chemtools

Python tools for quantum chemical calculations

poremapper

cavity shape and size mapping by growing a guest inside a host

xdimer

Simulation of multi-molecular emission spectra dominated by intermolecular vibrations

imd-cookie-cutter

A tool for removing atoms in IMD config files, just like a cookie cutter in higher dimensions

mlx-atomistic

Apple Silicon-native molecular dynamics and DFT runtime built on MLX and Metal — the GPU on your Mac, no CUDA or cloud.