Software for molecular mechanics modeling
From Wikipedia, the free encyclopedia
[edit] 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 | License | |
|---|---|---|---|---|---|---|---|---|
| AGM Build | Y | Y | Model building with charges and MM atom types | |||||
| AMBER | Y | Y | Y | |||||
| Ascalaph | Y | Y | Y | I | Molecular builder: DNA, proteins, hydrocarbons, nanotubes. | |||
| BOSS | Y | Y | Y | OPLS | ||||
| CHARMM | Y | Y | Y | Y | I | |||
| ChemSketch | Y | Y | Y | Fast 2-D graphical molecule builder and 3-D viewer. Contains simplified CHARMM for fast stable inaccurate optimization of single molecules up to 1000 atoms | ||||
| 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 | ||
| MOLDY | Y | Parallel, only pair-potentials, Cell lists, modified Beeman's algorithm | ||||||
| NAB | Y | Generation of Models for "Unusual" DNA and RNA | ||||||
| Packmol | Y | Builds complex initial configurations for Molecular Dynamics | ||||||
| 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 | |
| UCSF_Chimera | Y | Visually appealing viewer | ||||||
| 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 |
