Suvarna Garge (Editor)

Abalone (molecular mechanics)

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Developer(s)
  
Agile Molecule

Operating system
  
Windows XP, 7

Development status
  
Active

Platform
  
x86, Nvidia GPU CUDA

Abalone (molecular mechanics)

Initial release
  
2006; 11 years ago (2006)

Stable release
  
1.9.0 / May 17, 2016; 9 months ago (2016-05-17)

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) or in implicit water models. Mainly designed to simulate the protein folding and DNA-ligand complexes in AMBER force field.

Key features

  • 3D molecular graphics
  • 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
  • Interface with quantum chemistry - ORCA, NWChem, Firefly (PC GAMESS), CP2K
  • GPU accelerated molecular modeling

    • References

    Abalone (molecular mechanics) Wikipedia
    (Text) CC BY-SA