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 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 Interface with quantum chemistry - ORCA, NWChem, Firefly (PC GAMESS), CP2K GPU accelerated molecular modeling
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Benchmarking