Leonard-jones parameters

Here Vij denotes the distance between atoms i and j and g(i) the type of the amino acid i. The Leonard-Jones parameters Vij,Rij for potential depths and equilibrium distance) depend on the type of the atom pair and were adjusted to satisfy constraints derived from as a set of 138 proteins of the PDB database [18, 17, 19]. The non-trivial electrostatic interactions in proteins are represented via group-specific dielectric constants ig(i),g(j) depending on the amino-acid to which atom i belongs). The partial charges qi and the dielectric constants were derived in a potential-of-mean-force approach [20]. Interactions with the solvent were first fit in a minimal solvent accessible surface model [21] parameterized by free energies per unit area (7j to reproduce the enthalpies of solvation of the Gly-X-Gly family of peptides [22]. Ai corresponds to the area of atom i that is in contact with a ficticious solvent. Hydrogen bonds are described via dipole-dipole interactions included in the electrostatic terms... 

Species MW MW 0) Leonard—Jones parameters Critical constants ... 

The binary diffusivity, D, of the reactants in which the Leonard-Jones parameters (o, Q) are available, is calculated through the Chapman-Enskog theory by,... 

CONH (amide), Leonard—Jones parameters Cieplak 1991 CONH (peptide)... 

Read the Leonard—Jones parameters for helium from Table B1 and B2 in Appendix B ... 

Leonard-Jones Parameters of the Linear Chain with Zero-Point Energy... 

Leonard - Jones parameters for the various pair potentials in a NaCl solution is given in A and in units of 10" ° erg. 

Here, k provides a measure of the anisotropy in the well depth and for rodlike molecules is the ratio 8 1 where and Eg are the well depths when the molecules are side-by-side and end-to-end, respectively. The scaling parameter Eq is the well depth when the molecules are in the cross configuration as we can see by setting u, uj = u, f = uj f = 0 in Eqs. (4), (6) and (7). We should note that in the limit k and k tend to unity, that is x and x vanish then the Gay-Berne potential is reduced to the Leonard-Jones 12-6 potential. 

It seems that the method to fix the size parameter of the Leonard-Jones potential to match the density of ambient water is unable to predict the internal energy of the high density phases of ice. 

Leonard-Jones potential - A simple but useful function for approximating the interaction between two neutral atoms or molecules separated by a distance r by writing the potential energy as U(r) = (rJry - rJrY, where e and are adjustable parameters. In this form the depth of the potential well is 8 and the minimum occurs at. The (l/r) term is often replaced by other powers of 1/r. 

An extensive reparameterization of the Coulomb and Leonard-Jones terms of the AMBER force field led to the development of the OPLS (see OPLS Force Fields) parameter set. In OPLS the majority of bond, angle, and torsion terms were kept at their standard AMBER values however, the atomic partial charges were empirically determined for small molecules and assumed to be transferable to larger molecules. This treatment of partial charge differs significantly from the approach used in AMBER, in which a unique set of partial charges is derived for each molecule from fitting to the quantum mechanical ESP. 

The Lennard-Jones type potential is used for the interaction between Fe atoms and lubricant molecules. The parameter c in the Leonard-Jones potential was changed in order to investigate the effect of the interaction between lubricants and the sur ces. There are oxide or any other contaminants present on actual solid sur ces, ndiich may make interaction between surface atoms and lubricant molecules weaker. The calculations are conducted by using the original value e, and the half value of E, denoted by E0.5. 

---