Abalone (molecular mechanics)
Protein model on Abalone
DNA model on Abalone
Abalone is a general purpose molecular dynamics and molecular graphics program for simulations of bio-molecules in a periodic boundary conditions in explicit water (Flexible SPC[1]) or in implicit water models.[2] Mainly designed to simulate the proteins folding and DNA-ligand complexes in AMBER force field.
The key features
- 3D molecular graphics
- Building and editing chemical structures
- Library of building blocks
- Force Fields: AMBER 94, 96, 99SB, 03; OPLS
- Geometry optimization
- Molecular dynamics with multiple time step integrator
- Hybrid Monte Carlo
- Replica exchange[3]
- Interface with quantum chemistry - ORCA, NWChem, Firefly, CP2K
- GPU accelerated molecular dynamics
See also
References
- ↑ Toukan K and 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.
- ↑ 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 and 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.
External links
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