VEGA ZZ is the evolution of the well known

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 current version of the code is Amber version 10, which is distributed by UCSF subject to a licensing agreement

YASARA is a molecular-graphics, -modeling and -simulation program for Windows, Linux and Mac OS X developed since 1993, that finally makes it really easy to answer your questions.

BALLView is a standalone molecular modeling and visualization application. It is also a framework for developing molecular visualization functionality. It is available free of charge under the GPL for Linux, Windows and MacOS.

GROMACS: a suite for fast, free and flexible molecular dynamics (for advanced users)

CHARMM (Chemistry at HARvard Macromolecular Mechanics) is a program for macromolecular dynamics and mechanics. It performs standard molecular dynamics in many different ensembles (e.g., NVE, NVT, NPT) using state-of-the-art algorithms for timestepping, long range force calculation and periodic images. CHARMM can be used for energy minimization, normal modes and crystal optimizations as well. The potential energy functions available for use with CHARMM have been extensively parameterized for simulations of proteins, nucleic acids and lipids.

The TINKER molecular modeling software is a complete and general package for molecular mechanics and dynamics, with some special features for biopolymers.

NAMD, recipient of a 2002 Gordon Bell Award, is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. Based on Charm++ parallel objects, NAMD scales to hundreds of processors on high-end parallel platforms and tens of processors on commodity clusters using gigabit ethernet. NAMD uses the popular molecular graphics program VMD for simulation setup and trajectory analysis, but is also file-compatible with AMBER, CHARMM, and X-PLOR. NAMD is distributed free of charge with source code. You can build NAMD yourself or download binaries for a wide variety of platforms. Our tutorials show you how to use NAMD and VMD for biomolecular modeling.

ProtoMol is an object-oriented, component based, framework for molecular dynamics (MD) simulations.