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. 

CIIARMM was first developed as a united atom force field and parameters for some amino acids have been published B. R. Brooks et al.. 1 Comp. ( hem.. 4, 1H7 fl9K3). Siihseqiient changes to the functional form and param eters h ave been published W. Reiher, Ph.D.. TIarvard but most recent parameter develop-... 

United Atom Force Fields and Reduced Representations... 

United atom force fields (see United versus All Atom Force Fields on page 28) are sometimes used for biomolecules to decrease the number of nonbonded interactions and the computation time. Another reason for using a simplified potential is to reduce the dimensionality of the potential energy surface. This, in turn, allows for more samples of the surface. 

AMBER was first developed as a united atom force field [S. J. Weiner et al., J. Am. Chem. Soc., 106, 765 (1984)] and later extended to include an all atom version [S. J. Weiner et al., J. Comp. Chem., 7, 230 (1986)]. HyperChem allows the user to switch back and forth between the united atom and all atom force fields as well as to mix the two force fields within the same molecule. Since the force field was developed for macromolecules, there are few atom types and parameters for small organic systems or inorganic systems, and most calculations on such systems with the AMBER force field will fail from lack of parameters. 

This force field was developed primarily for protein and nucleic acid applications. It is a united atom force field, and there are many versions. Once again, you might like to see the Abstract of the original Paper. 

Improvement is apparent over the AMBER united-atom force field which has previously been demonstrated to be superior to many alternatives. 

Force fields split naturally into two main classes all-atom force fields and united atom force fields. In the former, each atom in the system is represented explicitly by potential functions. In the latter, hydrogens attached to heavy atoms (such as carbon) are removed. In their place single united (or extended) atom potentials are used. In this type of force field a CH2 group would appear as a single spherical atom. United atom sites have the advantage of greatly reducing the number of interaction sites in the molecule, but in certain cases can seriously limit the accuracy of the force field. United atom force fields are most usually required for the most computationally expensive tasks, such as the simulation of bulk liquid crystal phases via molecular dynamics or Monte Carlo methods (see Sect. 5.1). 

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],... 

Table 5.1 Parameters of the united atom force field for polyethylene used as the atomistic input for the coarse-graining procedure. The Lennard-Jones parameters pertain to CH2-group interaction, since chain ends were not considered in the coarse-graining. 

From a procedural standpoint, the start and stop residues of each of the seven helices was first identified by hydropathy analysis by using Kyte-Doolittle19 hydropathy indices. Each of the seven helices was then built individually, essential hydrogens were added, and the peptides were minimized with the Kollman United Atoms force field within the Sybyl software suite (Tripos Associates, Inc.). Typically, steepest descent was used initially as the minimization method (25-50... 

Force fields for biological macromolecules fall into two classes united-atom, and all-atom force fields. All-atom force fields, as the name suggests, represent all atoms in a protein explicitly. United-atom force fields, on the other hand, treat only heavy (non-hydrogen) atoms and polar hydrogen atoms explicitly, while nonpolar hydrogen atoms are not represented explicitly, but rather represented as part of the carbon atom to which they are bonded (which will have an enlarged van der Waals radius (Lennard-Jones collision diameter)). 

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... 

Shah et al. carried out a Monte-Carlo simulation in the isothermal-isobaric (NPT) ensemble of [C4mim][PF6] [12]. The authors calculated the molar volume, cohesive energy density, isothermal compressibility, cubic expansion coefficient, and liquid structure as a function of temperature and pressure. A united atom force field was developed using a combination of ab initio calculations and literature parameter values were also developed. Calculated molar volumes were within 5% of experimental values, and a reasonable agreement was obtained between calculated and experimental values of the isothermal compressibility and cubic expansion coefficient. [PF6] anions were found to cluster preferentially in two favorable regions near the cation, namely around the C2 carbon atom, both below and above the plane of the imidazole ring [12],... 

In a united atom force field the van der Waals centre of the united atom is usually associated with the position of the heavy (i.e. non-hydrogen) atom. Thus, for a united CH3 or CH2 group the van der Waals centre would be located at the carbon atom. It would be more accurate to associate the van der Waals centre with a position that was offset slightly from the carbon position, in order to reflect the presence of the hydrogen atoms. Toxvaerd has developed such a model that gives superior performance for alkanes than do the simple united atom models, particularly for simulations at high pressures [Toxvaerd 1990]. In... 

Fig 4 43 The interaction energy between the two arrangements shown is equal in a traditional united atom force field but different in the Toxvaerd anisotropic model (Figure adapted from Toxvaerd S 1990 Molecular Dynamics Calculations of the Equation cf State of Alkanes The Journal of Chemical Physics 93-4290-4295 )... 

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