Amber (Assisted Model Building with Energy Refinement) "Amber" refers to two things: a set of molecular mechanical force fields for the simulation of biomolecules (which are in the public domain, and are used in a variety of simulation programs); and a package of molecular simulation programs which includes source code and demos.

AutoDock Vina is an open-source program for doing molecular docking.

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.

LAMMPS is a classical molecular dynamics code, and an acronym for Large-scale Atomic/Molecular Massively Parallel Simulator.

NAMD is a molecular dynamics program.

OpenKIM is a library of functions that implements and api for KIM (Knowledgebase of Interatomic Models), which is used by some molecular simulation codes.

OpenMM is a library of molecular mechanics functions for GPU chips. It is used to install the GPU capable versions of GROMACS and AMBER.

The QUIP package is a collection of software tools to carry out molecular dynamics simulations. It implements a variety of interatomic potentials and tight binding quantum mechanics.