OPLS force fields united-atom

United Atom force fieldsare used often for biological polymers. In th esc m oleciiles, a reduced ii nm ber of explicit h ydrogen s can have a notable effect on the speed of the calculation. Both the BlOn and OPLS force fields are United Atom force fields. AMBER con tain s both aU nited and an All Atom force field. 

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. 

The optimized potentials for liquid simulations (OPLS) force field can be divided into the OPLS-UA (united-atom) [96, 110-112] and the OPLS-AA (all-atom) [57, 67, 92, 103, 135-139] versions. Among the two, the OPLS-UA force field is predominantly used for engineering applications, mainly because it is computatirMi-ally cheaper than the all-atom version. The OPLS-UA force field is available for hydrocarbons [96], amides [110], peptides [110], alcohols [111], or proteins [112]. The OPLS-AA force field was parameterized for small organic molecules and is intended for biochemical applications. The parameters of the OPLS-AA force field are available for a broader range of functional groups and molecules. Thus, besides hydrocarbons [103] and alcohols [57], parameters can be found for thiols [57], sulfides [57], ketones [57], amides [57], amines [139], pyrrole [138], furan [138], diazoles [138], oxazoles [138], proteins [67], and carbohydrates [92], among others. 

Equations (8-13) and the associated parameters constitute a force field (see Force Fields A Brief Introduction and Force Fields A General Discussion). There are both all-atom and united-atom models the former have an interaction site i at the nucleus of each atom, while the latter retain the all-atom description except for hydrogens on saturated carbon, which are taken as implicit. The parameters for the most successful force fields for liquid simulations have been developed to yield simultaneously excellent descriptions of molecular structure, conformational energetics, intermolecular interaction energies, and properties of fluids including densities, heats of vaporization, and free energies of solvation (see OPLS Force Fields). 

Jorgensen et al. has developed a series of united atom intermolecular potential functions based on multiple Monte Carlo simulations of small molecules [10-23]. Careful optimisation of these functions has been possible by fitting to the thermodynamic properties of the materials studied. Combining these OPLS functions (Optimised Potentials for Liquid Simulation) with the AMBER intramolecular force field provides a powerful united-atom force field [24] which has been used in bulk simulations of liquid crystals [25-27],... 

Examples of united-atom protein force-fields for proteins are GROMOS87 and 96,21,48 CHARMM PARAM19,49 OPLS/UA (united atom)50 and the original force fields developed for the AMBER program.51 United atom force fields were developed to reduce the computer time required for molecular dynamics simulations by reducing the number of atoms. They are still... 

To study the vibrational energy relaxation of the amide I mode in N-methylacetamide, we employed the OPLS all-atom force field to model the solute and the flexible simple-point-charge (SPC) water modeF with doubled hydrogen masses to model the solvent D2O. To investigate the photoinduced heat transfer in photoswitchable peptides, we used the GROMOS96 united atom force field 43al. Additional force field parameters for the azobenzene unit were derived from density functional theory as described in Ref. [32]. We employed a united-atom modeP to describe the DMSO solvent, the SPC modeP to describe water, and the rigid all-atom model of Ref [57] to describe the chloroform solvent. 

Some force fields for MM calculations on biomolecules (for example, OPLS, AMBER, CHARMM) exist in both united-atom (UA) and all-atom (AA) versions. A UA force field saves computational time by not explicitly including hydrogen atoms bonded to aliphatic carbon atoms. Instead, the field contains parameters for the CHj, CH2, and CH groups. 

The intramolecular parameters kf,ro, kg, and 0q from the AMBER force field [21, 22] were used. The oxygen atoms of alcohols and ethers were described by the OPLS parameters [17,18]. The Lennard-Jones parameters for halogens and the atoms of the aliphatic groups were optimized to reproduce the experimentally measured solubilities of methane and its halogenated derivatives in water and hexane, separately [23]. The resulting parameters do not follow the standard combination rules because we were unable to find a set of parameters consistent with the rules which would yield sufficiently accurate solubilities of the solutes in both phases. A similar difficulty was encountered in other studies of interfacial systems, in which the united atom representation was used to describe nonpolar molecules [24, 25]. 

AMBER/OPLS united atom force field ° °" and with an implicit GB/SA solvent model.The SDE method does not yield equilibrium-free energy surfaces for folding. It does, however, allow for a study of the direct sequence of events connecting an unfolded conformation to the folded state. 

The observation that most common united-atom force fields seem to lead to a density that is too high, led Berger et al. to re-parameterize a force field for DPPC starting with the GROMOS bonded parameters, the OPLS nonbonded parameters and three different sets of partial charges. The Lennard-Jones parameters for the hydrocarbon tails were determined from pentadecane simulations. The final choice of these authors results in a density that agrees within % with the experimental density. ... 

The latter nonbonded interactions are also evaluated between intermolecular atom pairs, and they are usually reduced by a factor of two for intramolecular 1,4-interactions. The parameters in the expressions are taken from the OPLS united-atom and all-atom force fields. They are extracted automatically from parameter files provided with the program. These files are easily edited to add new parameters. If any parameters are missing, warnings are issued by the program. 

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