MD

Autodock: Automated docking tools.​

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MDAnalysis: Python library to analyze trajectories from molecular dynamics simulations.

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VMD: Molecular modelling, visualization, and analysis program.

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Chimera: Visualization and analysis of molecular structures and related data.

Gromacs: MD package mainly designed for simulations of proteins, lipids, and nucleic acids.

QM

​ORCA: provides cutting-edge methods in the field of electronic structure theory, including DFT and correlated wave function-based methods.

Avogadro: Advanced molecule editor and visualizer designed for cross-platform use in molecular modeling, bioinformatics, materials science, and related areas.

VESTA: 3D visualization program for structural models, volumetric data such as electron/nuclear densities, and crystal morphologies.