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.

The activation-relaxation technique (ART) is an open-ended search method for finding local transition states.

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

This software package is designed for performing Molecular Simulations of gases, liquids and mixtures using state of the art Continuous Fractional Component Monte Carlo techniques.

DOCK (also called UCSF Dock) is molecular modeling program used to identify potential binding geometries and interactions of a molecule to a target.

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.

HOOMD-blue is a general-purpose particle simulation toolkit optimized for execution on both GPUs and CPUs.

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