Solvent design simulation

The diffusive behavior of a particle can be modeled using the Langevin equation. For example, in certain reactions, the two reactants must come into contact in order for a reaction to take place. In these types of reactions the rate-determining step may be due to the diffusion of the two reactants in the solvent. Computer simulations, commonly known as Brownian dynamics simulations, are employed at th molecular level to study these diffusion-controlled processes and aid in design of systems with prescribed transport or kinetic properties. 

OPTS (Optim i/.ed Potentials for Liquid Simulations) is based on a force field developed by the research group of Bill Jorgensen now at Yale University and previously at Purdue University. Like AMBER, the OPLS force field is designed for calculations on proteins an d nucleic acids. It in troduces non bonded in leraclion parameters that have been carefully developed from extensive Monte Carlo liquid sim u lation s of small molecules. These n on-bonded interactions have been added to the bonding interactions of AMBER to produce a new force field that is expected to be better than AMBER at describing simulations w here the solvent isexplic-... 

These models are designed to reproduce the random movement of flexible polymer chains in a solvent or melt in a more or less realistic way. Simulational results which reproduce in simple cases the so-called Rouse [49] or Zimm [50] dynamics, depending on whether hydrodynamic interactions in the system are neglected or not, appear appropriate for studying diffusion, relaxation, and transport properties in general. In all dynamic models the monomers perform small displacements per unit time while the connectivity of the chains is preserved during the simulation. 

The potential energy function prohibits double occupancy of any site on the 2nnd lattice. In the initial formulation, which was designed for the simulation of infinitely dilute chains in a structureless medium that behaves as a solvent, the remaining part of the potential energy function contains a finite repulsion for sites that are one lattice unit apart, and a finite attraction for sites that are two lattice units apart [153]. The finite interaction energies for these two types of sites were obtained by generalizing the lattice formulation of the second virial coefficient, B2, described by Post and Zimm as [159] ... 

---