OpenMM is a toolkit for molecular simulation using high performance GPU code.

Open Babel is a chemical toolbox designed to speak the many languages of chemical data.

Open-Source Quantum Chemistry – an electronic structure package in C++ driven by Python

Libint: high-performance library for computing Gaussian integrals in quantum mechanics

Avogadro is an advanced molecular editor designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas.

Biomolecular simulation trajectory/data analysis.

A program implementing the Hartree–Fock (also post-HF: MP2, CCSD(T), CIS and TDHF/RPA)/self-consistent field method (also DIIS) with Gaussian orbitals

ERKALE -- HF/DFT from Hel