Pair potential

About: Pair potential is a research topic. Over the lifetime, 2720 publications have been published within this topic receiving 82153 citations.

Interaction Models for Water in Relation to Protein Hydration

Abstract: For molecular dynamics simulations of hydrated proteins a simple yet reliable model for the intermolecular potential for water is required. Such a model must be an effective pair potential valid for liquid densities that takes average many-body interactions into account. We have developed a three-point charge model (on hydrogen and oxygen positions) with a Lennard-Jones 6–12 potential on the oxygen positions only. Parameters for the model were determined from 12 molecular dynamics runs covering the two-dimensional parameter space of charge and oxygen repulsion. Both potential energy and pressure were required to coincide with experimental values. The model has very satisfactory properties, is easily incorporated into protein-water potentials, and requires only 0.25 sec computertime per dynamics step (for 216 molecules) on a CRAY-1 computer.

Bond-orientational order in liquids and glasses

Abstract: Bond-orientational order in molecular-dynamics simulations of supercooled liquids and in models of metallic glasses is studied. Quadratic and third-order invariants formed from bond spherical harmonics allow quantitative measures of cluster symmetries in these systems. A state with short-range translational order, but extended correlations in the orientations of particle clusters, starts to develop about 10% below the equilibrium melting temperature in a supercooled Lennard-Jones liquid. The order is predominantly icosahedral, although there is also a cubic component which we attribute to the periodic boundary conditions. Results are obtained for liquids cooled in an icosahedral pair potential as well. Only a modest amount of orientational order appears in a relaxed Finney dense-random-packing model. In contrast, we find essentially perfect icosahedral bond correlations in alternative "amorphon" cluster models of glass structure.

Some Topics in the Theory of Fluids

Abstract: It is shown how certain thermodynamic functions, and also the radial distribution function, can be expressed in terms of the potential energy distribution in a fluid. A miscellany of results is derived from this unified point of view. (i) With g(r) the radial distribution function and Φ(r) the pair potential, it is shown that g exp (Φ/kT) may be written as a Fourier integral, or as a power series in r2 the terms of which alternate in sign. (ii) A potential‐energy distribution which is independent of the temperature implies an equation of state which is a generalization of a number of well‐known approximations. (iii) The grand partition function of the one‐dimensional lattice gas is obtained from thermodynamic arguments without evaluating a sum over states. (iv) If in a two‐dimensional honeycomb (three‐coordinates) lattice gas fr(r=0, 1, 2, 3) is the fraction of all the empty sites which at equilibrium are neighbored by exactly r filled sites, then at the critical density the values of all four of the f's ...

Fluids with highly directional attractive forces. I. Statistical thermodynamics

Abstract: A new formulation of statistical thermodynamics is derived for classical fluids of molecules that tend to associate into dimers and possibly highers-mers due to highly directional attraction. A breakup of the pair potential into repulsive and highly directionally attractive parts is introduced into the expansion of the logarithm of the grand partition function in fugacity graphs. The bonding by the directional attraction is used to classify the graphs and to introduce a topological reduction which results in the replacement of the fugacity by two variables: singlet densityρ and monomer densityρ 0. Results for the thermodynamic functions as functionals ofρ andρ 0 are given in the form of graph sums. Pair correlations are analyzed in terms of a new matrix analog of the direct correlation function. It is shown that the low-density limit is treated exactly, while major difficulties arise when the Mayer expansion, which employs onlyp, is used. The intricate resummations required for the Mayer expansion are illustrated for the case where dimers are the only association products.

Improved simulation of liquid water by molecular dynamics

Abstract: Molecular dynamics calculations on a classical model for liquid water have been carried out at mass density 1 g/cm3 and at four temperatures. The effective pair potential employed is based on a four‐charge model for each molecule and represents a modification of the prior ``BNS'' interaction. Results for molecular structure and thermodynamic properties indicate that the modification improves the fidelity of the molecular dynamics simulation. In particular, the present version leads to a density maximum near 27°C for the liquid in coexistence with its vapor and to molecular distribution functions in better agreement with x‐ray scattering experiments.