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Short list of molecular mechanics programs
Min - Optimization, MD - Molecular Dynamics, MC - Monte Carlo, QM - Quantum mechanics. HA - Hardware accelerated.
Y - Yes.
I - Has interface.
| View
3D |
Model
Builder |
Min | MD | MC | QM | HA | Comments | License | |
|---|---|---|---|---|---|---|---|---|---|
| AGM Build | Y | Y | Model building with charges and MM atom types | Free (GPL) | |||||
| AMBER | Y | Y | Y | ||||||
| Ascalaph | Y | Y | Y | Y | I | Y | Molecular building (DNA, proteins, hydrocarbons, nanotubes). Molecular dynamics. GPU acceleration. |
||
| 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 | |||||
| COSMOS | Y | Y | Y | Y | Y | I | Hybrid QM/MM COSMOS-NMR force field with fast semi-empirical calculation of electrostatic and/or NMR properties. 3-D graphical molecule builder and 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 | |||||||
| MacroModel | Y | Y | Y | Y | Y | I | OPLS-AA, GBSA solvent model, conformational sampling, minimization, MD | ||
| Materials Studio | Y | Y | Y | Y | Y | Y | Materials Studio is a software environment that brings the materials simulation technology to desktop computing, solving key problems throughout the R&D process. | Closed source/Trial avail. | |
| 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 | |||
| MOIL | Y | Y | Y | Y | Also includes action-based algorithms (Stochastic Difference Equation in Time and Stochastic Difference Equation in Length) and locally enhanced sampling. | ||||
| molecools | Y | Y | Simple Javascript molecular visualization tool. | ||||||
| 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 | |||||||
| Prime | Y | Y | Y | Y | I | Homology modeling, loop and side chain optimization, minimization, OPLS-AA, SGB solvent model, parallalized | |||
| 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 | |||||||
| STR3DI32 | Y | Y | Y | Y | ' | ' | Sophisticated molecular 3-D builder and viewer, advanced structure analytical routines, full featured molecular modeling, including docking and the handling of complexes. | ||
| TINKER | I | Y | Y | Y | Y | I | Software Tools for Molecular Design | ||
| UCSF Chimera | Y | Y | Y | Visually appealing viewer, amino acid rotamers and other building, includes Antechamber and MMTK, Ambertools plugins in development. | |||||
| VMD + NAMD | Y | Y | Y | Y | ? | Fast, parallel MD | |||
| WHAT IF | Y | Y | I | I | I | Visualizer for MD. Interface to GROMACS. | |||
| xeo | Y | Y | open project management for nanostructures | ||||||
| YASARA | Y | Y | Y | Y | Molecular-graphics, -modeling and -simulation program | ||||
| Zodiac | Y | Y | Y | Drug design suite |
See also
Chemical software catalogs
- SINCRIS
- Linux4Chemistry
- Collaborative Computational Project
- World Index of Molecular Visualization Resources
- Short list of Molecular Modeling resources
- OpenScience
- Biological Magnetic Resonance Data Bank
Wikipedia content modification information:
- This page was last modified on 15 November 2008, at 14:09.
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