Abalone (molecular mechanics): Difference between revisions
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* {{Official website|www.biomolecular-modeling.com/Abalone}}<!--Sometimes down for a day or two.--> |
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* [http://www.biomolecular-modeling.com/Abalone/Benchmarking.html Benchmarking] |
* [http://www.biomolecular-modeling.com/Abalone/Benchmarking.html Benchmarking] |
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[[Category:Monte Carlo software]] |
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[[Category:Bioinformatics software]] |
[[Category:Bioinformatics software]] |
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[[Category:Computational chemistry software]] |
[[Category:Computational chemistry software]] |
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Revision as of 22:31, 7 August 2018
| Developer(s) | Agile Molecule |
|---|---|
| Initial release | 2006 |
| Stable release | 1.9.0
/ May 17, 2016 |
| Operating system | Windows XP, 7 |
| Platform | x86, Nvidia GPU CUDA |
| Available in | English |
| Type | Molecular dynamics, molecular graphics |
| License | Proprietary |
| Website | www |
Abalone is a general purpose molecular dynamics and molecular graphics program for simulations of bio-molecules in a periodic boundary conditions in explicit (flexible SPC water model[1]) or in implicit water models.[2] Mainly designed to simulate the protein folding and DNA-ligand complexes in AMBER force field.
Key features
- 3D molecular graphics
- Automatic Force Field generator for bioelements: H, C, N, O]
- Building and editing chemical structures
- Library of building blocks
- Force fields: Assisted Model Building with Energy Refinement (AMBER) 94, 96, 99SB, 03; Optimized Potentials for Liquid Simulations (OPLS)
- Geometry optimizing
- Molecular dynamics with multiple time step integrator
- Hybrid Monte Carlo
- Replica exchange[3]
- Interface with quantum chemistry - ORCA, NWChem, Firefly (PC GAMESS), CP2K
- GPU accelerated molecular modeling
See also
References
- ^ Toukan K; Rahman A (1985). "Molecular-dynamics study of atomic motions in water". Physical Review B. 31 (5): 2643–2648. Bibcode:1985PhRvB..31.2643T. doi:10.1103/PhysRevB.31.2643.
{{cite journal}}: Unknown parameter|last-author-amp=ignored (|name-list-style=suggested) (help) - ^ Still WC, Tempczyk A, Hawley RC, Hendrickson T (1990). "Semianalytical treatment of solvation for molecular mechanics and dynamics". J Am Chem Soc. 112 (16): 6127–6129. doi:10.1021/ja00172a038.
- ^ Y. Sugita; Y. Okamoto (1999). "Replica-exchange molecular dynamics method for protein folding". Chemical Physics Letters. 314: 141–151. Bibcode:1999CPL...314..141S. doi:10.1016/S0009-2614(99)01123-9.
{{cite journal}}: Unknown parameter|last-author-amp=ignored (|name-list-style=suggested) (help)