Force field 6-12 Lennard-Jones potential

Atomistically detailed models account for all atoms. The force field contains additive contributions specified in tenns of bond lengtlis, bond angles, torsional angles and possible crosstenns. It also includes non-bonded contributions as tire sum of van der Waals interactions, often described by Lennard-Jones potentials, and Coulomb interactions. Atomistic simulations are successfully used to predict tire transport properties of small molecules in glassy polymers, to calculate elastic moduli and to study plastic defonnation and local motion in quasi-static simulations [fy7, ( ]. The atomistic models are also useful to interiDret scattering data [fyl] and NMR measurements [70] in tenns of local order. 

Ihi.. same molecule but separated by at least three bonds (i.e. have a 1, h relationship where n > 4). In a simple force field the non-bonded term is usually modelled using a Coulomb piilential term for electrostatic interactions and a Lennard-Jones potential for van der IV.uls interactions. 

Some force fields replace the Lennard-Jones 6-12 term between hydrogen-bonding atoms by ail explicit hydrogen-bonding term, which is often described using a 10-12 Lennard-Jones potential ... 

Most force fields employ the Lennard-Jones potential, despite the known inferiority to an exponential type function. Let us examine the reason for this in a little more detail. 

The major forms of van der Waals forces between molecules that are not bonded together are the permanent dipole-dipole interaction, the dispersion-induced temporary dipole interaction, and the hydrogen bond. They are short-range forces that operate only when two atoms or molecules are in close proximity. The Lennard-Jones potential of 6-12 is a model of this potential field ... 

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. 

The Lennard-Jones potential continues to be used in many force fields, particularly those targeted for use in large systems, e.g., biomolecular force fields. In more general force fields targeted at molecules of small to medium size, slightly more complicated functional forms, arguably having more physical justification, tend to be used (computational times for small molecules are so short dial the efficiency of the Lennard-Jones potential is of little consequence). Such forms include the Morse potential [Eq. (2.5)] and the Hill potential... 

The last term in the formula (1-196) describes electrostatic and Van der Waals interactions between atoms. In the Amber force field the Van der Waals interactions are approximated by the Lennard-Jones potential with appropriate Atj and force field parameters parametrized for monoatomic systems, i.e. i = j. Mixing rules are applied to obtain parameters for pairs of different atom types. Cornell et al.300 determined the parameters of various Lenard-Jones potentials by extensive Monte Carlo simulations for a number of simple liquids containing all necessary atom types in order to reproduce densities and enthalpies of vaporization of these liquids. Finally, the energy of electrostatic interactions between non-bonded atoms is calculated using a simple classical Coulomb potential with the partial atomic charges qt and q, obtained, e.g. by fitting them to reproduce the electrostatic potential around the molecule. 

Short-range repulsions and London dispersion attractions are balanced by a shallow energy minimum at the van der Waals distance (Eq. (8)), describing the Lennard Jones potential, used by most force fields. Here the parameters A and B are calculated based on atomic radii and the minimum found at the sum of the two radii. 

Many molecular modelling techraques that use force-field models require the derivatives of the energy (i e the force) to be calculated with respect to the coordinates. It is preferable that analytical expressions for these derivatives are available because they are more accurate and faster than numerical derivatives. A molecular mechanics energy is usually expressed in terms of a combination of internal coordinates of the system (bonds, angles, torsions, etc.) and interatomic distances (for the non-bonded interactions). The atomic positions in molecular mechanics are invariably expressed in terms of Cartesian coordinates (unlike quantum mechanics, where internal coordinates are often used). The calculation of derivatives with respect to the atomic coordinates usually requires the chain rule to be applied. For example, for an energy function that depends upon the separation between two atoms (such as the Lennard-Jones potential. Coulomb electrostatic interaction or bond-stretching term) we can write ... 

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