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.
AutoDock is a suite of automated docking tools. It is designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure.
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.
MODELLER is used for homology or comparative modeling of protein three-dimensional structures.
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.