Written in C, AMMP is a modern full-featured molecular mechanics, dynamics and modeling program. It can manipulate both small molecules and macromolecules including proteins, nucleic acids and other polymers. The source code is available.

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. C and C++ source code is available.

B is a Java-based, on-line biomolecular modeling package. It should be useful in generating initial structures of biopolymers and small organic molecules. Simple force-field energy minimizations can be carried out in addition to simulated annealing with molecular dynamics.

CAChe is a computer-aided molecular design modeling tool which is derived from classical mechanics and quantum mechanics. Commercial package.

DYNAMO is a library of Fortran 90 modules that has been designed for the simulation of molecular systems using molecular mechanical (MM) and hybrid quantum mechanical (QM)/MM potential energy functions.

FANTOM calculates low-energy conformations of polypeptides and proteins, compatible with distance and dihedral angle constraints obtained typically from NMR experiments. Free software package for academic users.

FlexX is a computer program for predicting protein-ligand interactions.

http://www.bmm.icnet.uk/docking/

GROMOS is a general-purpose molecular dynamics computer simulation package for the study of biomolecular systems. No cost for academics.

GULP is a program for performing a variety of types of simulation on 3D periodic solids, gas phase clusters and isolated defects in a bulk material.

HyperChem is a sophisticated molecular modeling environment which unite 3D visualization and animation with quantum chemical calculations, molecular mechanics, and dynamics.
A commercial package

MacroModel combines leading force fields, accurate effective solvation models, and advanced conformational searching methods to provide a complete molecular modeling package suitable for a wide array of research.
A commercial package.

http://europa.chem.uga.edu/allinger/mm2mm3.html

MOE is a comprehensive software system for computer-assisted drug discovery. MOE combines visualization, simulation and application development in one package.

MODELLER is used for homology or comparative modeling of protein three-dimensional structures.

Moloc is a molecular modeling package designed with emphasis on high interactivity.

SYBYL's completely integrated environment for computational chemistry and molecular modeling provides the fundamental components for understanding molecular structure and properties with a special focus on the creation of new chemical entities.

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

X-PLOR is a program system for computational structural biology. X-PLOR stands for exploration of conformational space of macromolecules restrained to regions allowed by combinations of empirical energy functions and experimental data. But it also stands for exploration of modern concepts of structured programming in macromolecular simulation.

MacroModel is an integrated software system for modeling organic and bioorganic molecules using molecular mechanics. A commercial package.

ICM-Pro contains an all atom internal coordinate force field and efficient algorithm to perform local and global energy optimization of small or large molecules with respect to an arbitrary subset of variables.

A molecular modeling, graphics, and drug design program.

Bodil is a modular, multi-platform software package for biomolecular visualization and modeling.

http://www.chemsw.com/13052.htm

http://www.ccl.net/cca/software/MS-DOS/molgen/

The program package is designed to construct crystal structures of low potential energy, using a molecular force field.

FANTOM calculate conformations of linear and cyclic polypeptides and proteins which have low conformational energies and are compatible with distance and dihedral angle constraints.

BOSS (Biochemical and Organic Simulation System) is a general purpose molecular modeling system that performs molecular mechanics (MM) calculations, Metropolis Monte Carlo (MC) statistical mechanics simulations, and semiempirical AM1, PM3, and PDDG/PM3 quantum mechanics (QM) calculations.
MCPRO performs Monte Carlo statistical mechanics simulations of peptides, proteins, and nucleic acids in solution; it was derived from BOSS, but makes extensive use of the concept of residues.
A commercial packages.

The GCMC program is used to perform a molecular simulation in the grand canonical ensemble.

Gibbs program computes the thermodynamic properties of two coexisting phases using the Gibbs ensemble Monte Carlo technique.

ORAC  is a program for the molecular dynamics simulation of atomistic models of complex molecular systems such as biomolecules.

DL_POLY is a package of subroutines, programs and data files, designed to facilitate molecular dynamics simulations of macromolecules, polymers, ionic systems and solutions on a distributed memory parallel computer.

A Parallel Program for Molecular Dynamics Simulations of Biomolecules.

GROMACS is a molecular dynamics package primarily designed for biomolecular systems such as proteins and lipids.

LAMMPS is a classical molecular dynamics code that models an ensemble of particles in a liquid, solid, or gaseous state. It can model atomic, polymeric, biological, metallic, or granular systems using a variety of force fields and boundary conditions.

http://www.vscht.cz/fch/software/macsimus/index.html
MACSIMUS's features are:
· pdb : PDB to MACSIMUS converter, residue and force field selection
· blend : Force field builder, energy minimizer, and more
· cook : Molecular dynamics

This is a general purpose molecular dynamics code for simulations of mixtures of either rigid or flexible molecules, interacting by AMBER-like force field in a periodic rectangular cell.

http://cbsu.tc.cornell.edu/software/moil/moil.html

Moldy is a general-purpose molecular dynamics simulation program. Useful for a wide range of simulation calculations of atomic, ionic and molecular systems.

NAMD, recipient of a 2002 Gordon Bell Award , is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems.

PMEMD is a new version of Sander that has been written with the major goal of improving performance in Particle Mesh Ewald molecular dynamics simulations and minimizations.

Q is a molecular dynamics package designed for free energy calculations in biomolecular systems.

YASARA is a molecular graphics, modeling and simulation package.

MOLSCAT is a code for quantum mechanical (coupled channel) solution of the nonreactive molecular scattering problem.

SOLVATE is a program to construct an atomic solvent environment model for a given atomic macromolecule model (solute) for use in molecular dynamics simulations.

A program for the analysis of protein structures and molecular dynamics simulations

MMC is a Metropolis Monte Carlo program for the simulation of molecular assemblies in the canonical, grand-canonical and isothermal-isobaric ensembles employing several convergence acceleration techniques (e.g., force-biased displacement, extension-biased and local torsion changes, preferential selection of solvent to be moved, cavity-biased insertion, virial-biased volume change).

ASE is an Atomistic Simulation Environment written in the python programming language. There are modules for: building atomic structures, molecular dynamics, structure optimization, analysis and much more. Five calculators are included in ASE interfaces: Dacapo, Asap, Siesta, GridPAW and MMTK.

Materials Explorer is a computationally powerful molecular dynamics and Monte Carlo software package pecifically designed to be an engineering tool to study materials with real-world applications.

Reverse Monte Carlo and pseudo simulated annealing code for ab initio crystal structure determination.

Model-Free Analysis of Protein Dynamics from Heteronuclear NMR Relaxation Data.

The mdxvu program is a molecular dynamics and molecular structure analysis code.

AGM Build is a molecular builder and conformational editor. AGM Build can be used for interactive model preparation for molecular dynamics simulations, including association of atom types and partial charges.