LAMMPS Molecular Dynamics Simulator
Abalone The main application is the modeling of biomolecules, in particular, proteins, lipids, and nucleic acids.
HOOMD-blue is a general-purpose particle simulation GROMACStoolkit. It scales from a single CPU core to thousands of GPUs.
GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.

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