Abalone (molecular mechanics)
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File:Chaperonin-1AON.png
Protein 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
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3
References
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