Software:Abalone (molecular mechanics)
From HandWiki
| Developer(s) | Agile Molecule |
|---|---|
| Initial release | 2006 |
| Stable release | 2.1.4.2
|
| Operating system | Windows XP/7/8/10 |
| 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. doi:10.1103/PhysRevB.31.2643. Bibcode: 1985PhRvB..31.2643T.
- ↑ "Semianalytical treatment of solvation for molecular mechanics and dynamics". J Am Chem Soc 112 (16): 6127–6129. 1990. doi:10.1021/ja00172a038.
- ↑ Y. Sugita; Y. Okamoto (1999). "Replica-exchange molecular dynamics method for protein folding". Chemical Physics Letters 314: 141–151. doi:10.1016/S0009-2614(99)01123-9. Bibcode: 1999CPL...314..141S.
External links
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