Abalone (molecular mechanics)

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.

Developer(s)Agile Molecule
Initial release2006 (2006)
Stable release
Operating systemWindows XP/7/8/10
Platformx86, Nvidia GPU CUDA
Available inEnglish
TypeMolecular dynamics, molecular graphics
Protein model on Abalone
DNA model on Abalone

Key features

See also

  • Comparison of software for molecular mechanics modeling
  • Molecular design software
  • Ascalaph Designer
  • MDynaMix
  • Tinker (software)
  • NAMD


  1. 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.
  2. 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.
  3. 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.
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