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.
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.
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.
MOBCAL is a program to calculate mobilities.
NAMD is a molecular dynamics program.