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 ) 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