BOSS

BOSS (Biochemical and Organic Simulation System). The BOSS program is a general purpose molecular modeling system that performs molecular mechanics (MM) calculations, Metropolis Monte Carlo (MC) statistical mechanics simulations, and semiempirical AM1, PM3, and PDDG/PM3 quantum mechanics (QM) calculations. The MM calculations cover energy minimizations, normal mode analysis, and conformational searching with the OPLS force fields. The MC simulations can be carried out for pure liquids, solutions, clusters, or gas-phase systems; typical applications include computing properties of a pure liquid, free energies of solvation, effects of solvation on relative energies of conformers, changes in free energies of solvation along reaction paths, and structures and relative free energies of binding for host-guest complexes. Free energy changes are computed from statistical perturbation (FEP) theory. Alternatively, the energetics of the solutes can be represented with the QM methods. Coordinate files are input/output in PDB or mol format for facile interfacing and display. Extensive capabilities are provided for easy setup of the solvent molecules from equilibrated boxes of twelve common solvents including TIP3P, TIP4P, and TIP5P water or from user-provided solvent boxes that are created by running a pure-liquid simulation

Keywords for this software

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References in zbMATH (referenced in 3 articles )

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  1. Younes Nejahi; Mohammad Soroush Barhaghi; Jason Mick; Brock Jackman; Kamel Rushaidat; Yuanzhe Li; Loren Schwiebert; Jeffrey Potoff: GOMC: GPU Optimized Monte Carlo for the simulation of phase equilibria and physical properties of complex fluids (2019) not zbMATH
  2. Mezei, Mihaly: Using force-field grids for sampling translation/rotation of partially rigid macromolecules (2017)
  3. Jorgensen, William L.; Tirado-Rives, Julian: Molecular modeling of organic and biomolecular systems using BOSS and MCPRO. (2005) ioport