Abalone (molecular mechanics)

Abalone
Developer(s)	Agile Molecule
Initial release	2006; 18 years ago
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.biomolecular-modeling.com/Abalone

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.

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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

[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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