Software for molecular mechanics modeling

Short list of molecular mechanics programs

Min - Optimization, MD - Molecular Dynamics, MC - Monte Carlo, QM - Quantum mechanics.

Y - Yes.
I - Has interface.

	View 3D	Model Builder	Min	MD	MC	QM	Comments
AGM Build	Y	Y					Model building with charges and MM atom types
AMBER		Y	Y	Y
BOSS			Y		Y	Y	OPLS
CHARMM		Y	Y	Y	Y	I
UCSF_Chimera	Y						Visually appealing viewer
GROMACS				Y			High performance MD
GROMOS			Y	Y			Geared towards biomolecules
LAMMPS				Y			Has potentials for soft and solid-state materials and coarse-grain systems
MCCCS Towhee					Y		Originally designed for the prediction of fluid phase equilibria
MDynaMix				Y			Parallel MD
MOE	Y	Y	Y	Y		I	Molecular Operating Environment
Packmol		Y					Builds complex initial configurations for Molecular Dynamics
NAB		Y					Generation of Models for "Unusual" DNA and RNA
Protein Local Optimization Program		Y	Y	Y	Y		Helix, loop, and side chain optimization. Fast energy minimization.
QMOL	Y						Protein viewer
RasMol	Y						Fast viewer
Raster3D	Y						High quality raster images
TINKER	I	Y	Y	Y	Y	I	Software Tools for Molecular Design
VMD + NAMD	Y	Y		Y			Fast, parallel MD
WHAT IF	Y	Y	I	I	I		Visualizer for MD. Interface to GROMACS.
YASARA	Y	Y		Y		Y	Molecular-graphics, -modeling and -simulation program