Lennard-Jones parameters used molecular dynamics simulations

Extension to many dimensions provides insight into more sophisticated aspects of the method and into the nature of molecular interactions. In the second stage of this unit, the students perform molecular dynamics simulations of 3-D van der Waals clusters of 125 atoms (or molecules). The interactions between atoms are modeled using the Lennard-Jones potentials with tabulated parameters. Only pairwise interactions are included in the force field. This potential is physically realistic and permits straightforward programming in the Mathcad environment. The entire program is approximately 50 lines of code, with about half simply setting the initial parameters. Thus the method of calculation is transparent to the student. 

Figure 2. Experimental and simulated fluorescence Stokes shift function 5(f) for coumarin 343 in water. The curve marked Aq is a classical molecular dynamics simulation result using a charge distribution difference, calculated by semiempirical quantum chemical methods, between ground and excited states. Also shown is a simulation for a neutral atomic solute with the Lennard-Jones parameters of the water oxygen atom (S°). (From Ref. 4.)...

Lennard-Jones potentials. Because it is not our intention to review all advantages and applications of these different functional forms and parameter sets, we shall focus our explanations to the well-known AMBER force field (2, 3). This parameter set is widely used, and has already been successfully applied to molecular dynamics simulations of various surfactant systems. 

In order to ascertain whether the 3-regime behavior observed in the experimental vibrational lifetimes is indeed a result of local density enhancements, Goodyear and Tucker [12] computed both vibrational lifetimes and local density enhancements from molecular dynamics simulation for a model solute-solvent SCF solution. These authors considered a diatomic solute in a 2-dimensional supercritical Lennard-Jones fluid of 1150 atoms (Fig. 1). In this model, each of the solute atoms was designated as a Lennard-Jones site, and the Lennard-Jones parameters between solute and solvent atoms were taken to be the same as those between solvent atoms. The vibrational lifetimes were computed using the standard, classical Landau-Teller expression [69,70,72,73,78], i.e. 

Equilibrium Systems. Magda et al (12.) have carried out an equilibrium molecular dynamics (MD) simulation on a 6-12 Lennard-Jones fluid In a silt pore described by Equation 41 with 6 = 1 with fluid particle Interactions given by Equation 42. They used the Monte Carlo results of Snook and van Me gen to set the mean pore density so that the chemical potential was the same In all the simulations. The parameters and conditions set In this work were = 27T , = a, r = 3.5a, kT/e = 1.2, and... 

The computer simulations employed the molecular dynamics technique, in which particles are moved deterministically by integrating their equations of motion. The system size was 864 Lennard-Jones atoms, of which one was the solute (see Table II for potential parameters). There were no solute-solute interactions. Periodic boundary conditions and the minimum image criterion were used (76). The cutoff radius for binary interactions was 3.5 G (see Table II). Potentials were truncated beyond the cutoff. 

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