Carbon force fields

This situation, despite the fact that reliability is increasing, is very undesirable. A considerable effort will be needed to revise the shape of the potential functions such that transferability is greatly enhanced and the number of atom types can be reduced. After all, there is only one type of carbon it has mass 12 and charge 6 and that is all that matters. What is obviously most needed is to incorporate essential many-body interactions in a proper way. In all present non-polarisable force fields many-body interactions are incorporated in an average way into pair-additive terms. In general, errors in one term are compensated by parameter adjustments in other terms, and the resulting force field is only valid for a limited range of environments. 

Fig. 1. The time evolution (top) and average cumulative difference (bottom) associated with the central dihedral angle of butane r (defined by the four carbon atoms), for trajectories differing initially in 10 , 10 , and 10 Angstoms of the Cartesian coordinates from a reference trajectory. The leap-frog/Verlet scheme at the timestep At = 1 fs is used in all cases, with an all-atom model comprised of bond-stretch, bond-angle, dihedral-angle, van der Waals, and electrostatic components, a.s specified by the AMBER force field within the INSIGHT/Discover program.

Hccausc of Ihc restricted availability of corn ptilation al resources, sorn e force fields use Un itcd. torn types, fli is type of force field represeri ts implicitly all hydrogens associated with a methyl, rn elli yieti e, or rn etii in e group. Th e van der Waals param eters for united atom carbons reflect the increased si/.e because of the implicit (included) hydrogens. 

The OPLS force field is described in twtt papers, one discussing parameters for proteins W. L. Jorgensen and J. Tirado-Rives,/. Amer. (. hem. Soc., 110, 1557 (iy8K) and on e discii ssin g param eters for n iicleotide bases [J. Pranata, S. Wiersch ke, and W. L. Jorgen sen. , /.. Amer. Chem. Soc.. 117, 281(1 ( 1991)1. The force field uses the united atom concept ftir many, but not all. hydrttgens attached to carbons to allow faster calculation s on macromolecular systems. The amino and nucleic acid residue templates in HyperChein automatically switch to a united atom representation where appropriate when th e OPLS option is selected. 

In some force fields the interaction sites are not all situated on the atomic nuclei. For example, in the MM2, MM3 and MM4 programs, the van der Waals centres of hydrogen atoms bonded to carbon are placed not at the nuclei but are approximately 10% along the bond towards the attached atom. The rationale for this is that the electron distribution about small atoms such as oxygen, fluorine and particularly hydrogen is distinctly non-spherical. The single electron from the hydrogen is involved in the bond to the adjacent atom and there are no other electrons that can contribute to the van der Waals interactions. Some force fields also require lone pairs to be defined on particular atoms these have their own van der Waals and electrostatic parameters. 

In order for the transferability of parameters to be a good description of the molecule, force fields use atom types. This means that a sp carbon will be described by different parameters than a. sp - carbon, and so on. Usually, atoms in aromatic rings are treated differently from sp atoms. Some force fields even parameterize atoms for specific functional groups. For example, the carbonyl oxygen in a carboxylic acid may be described by different parameters than the carbonyl oxygen in a ketone. 

Quantum mechanical calculations generally have only one carbon atom type, compared with the many types of carbon atoms associated with a molecular mechanics force field like AMBER. Therefore, the number of quantum mechanics parameters needed for all possible molecules is much smaller. In principle, very accurate quantum mechanical calculations need no parameters at all, except fundamental constants such as the speed of light, etc. 

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