BOSS is a general-purpose molecular modeling program that performs molecular mechanics

Molecular mechanics

Molecular mechanics uses Newtonian mechanics to model molecular systems. The potential energy of all systems in molecular mechanics is calculated using force fields...

 calculations, Metropolis Monte Carlo

Monte Carlo method

Monte Carlo methods are a class of computational algorithms that rely on repeated random sampling to compute their results. Monte Carlo methods are often used in computer simulations of physical and mathematical systems...

 statistical mechanics simulations, and semiempirical AM1, PM3

PM3 (chemistry)

PM3, or Parameterized Model number 3, is a semi-empirical method for the quantum calculation of molecular electronic structure in computational chemistry. It is based on the Neglect of Differential Diatomic Overlap integral approximation....

, and PDDG/PM3 quantum mechanics

Quantum mechanics

Quantum mechanics, also known as quantum physics or quantum theory, is a branch of physics providing a mathematical description of much of the dual particle-like and wave-like behavior and interactions of energy and matter. It departs from classical mechanics primarily at the atomic and subatomic...

 calculations. The molecular mechanics calculations cover energy minimizations, normal mode analysis and conformational searching with the OPLS

OPLS

The OPLS force field was developed by Prof. William L. Jorgensen at Purdue University and later at Yale University.-Functional form:The functional form of the OPLS force field is very similar to that of AMBER:...

 force fields. BOSS is developed by Prof. William L. Jorgensen

William L. Jorgensen

William L. Jorgensen is a Sterling Professor of Chemistry at Yale University. He is considered a pioneer in the field of computational chemistry...

 at Yale University

Yale University

Yale University is a private, Ivy League university located in New Haven, Connecticut, United States. Founded in 1701 in the Colony of Connecticut, the university is the third-oldest institution of higher education in the United States...

.

Key features

• OPLS
  OPLS
  The OPLS force field was developed by Prof. William L. Jorgensen at Purdue University and later at Yale University.-Functional form:The functional form of the OPLS force field is very similar to that of AMBER:...
  
    Force Field
  Force field (chemistry)
  In the context of molecular modeling, a force field refers to the form and parameters of mathematical functions used to describe the potential energy of a system of particles . Force field functions and parameter sets are derived from both experimental work and high-level quantum mechanical...
  
   inventor
• Geometry optimization
• Semiempirical quantum chemistry
• MC simulations for pure liquids, solutions, clusters or gas-phase systems
• Free energy are computed from statistical perturbation (FEP
  Free energy perturbation
  Free energy perturbation theory is a method based on statistical mechanics that is used in computational chemistry for computing free energy differences from molecular dynamics or Metropolis Monte Carlo simulations. The FEP method was introduced by R. W. Zwanzig in 1954...
  
  ) theory
• TIP3P, TIP4P and TIP5P water models
  Water model
  In computational chemistry, classical water models are used for the simulation of water clusters, liquid water, and aqueous solutions with explicit solvent. These models use the approximations of molecular mechanics...
  
  

See also