Force fields all-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. 

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. 

Weiner, S.J. Kollman, P.A. Nguyen, D.T. Case, D.A. An all atom force field for simulations of proteins and nucleic acids J. Comput. Chem. 7 230-252,1986. 

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. 

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). 

Three other all-atom force fields have also received much recent attention in the literature MMFF94 [36-40], AMBER94 [9] and OPLS-AA [41, 42] and are becoming widely used. The latter two force fields both use non-bonded parameters which have been adjusted in order to reproduce experimental liquid phase densities and heats of vaporisation of small organic molecules. For example, OPLS-AA includes calculations on alkanes, alkenes, alcohols. 

The rapid rise in computer speed over recent years has led to atom-based simulations of liquid crystals becoming an important new area of research. Molecular mechanics and Monte Carlo studies of isolated liquid crystal molecules are now routine. However, care must be taken to model properly the influence of a nematic mean field if information about molecular structure in a mesophase is required. The current state-of-the-art consists of studies of (in the order of) 100 molecules in the bulk, in contact with a surface, or in a bilayer in contact with a solvent. Current simulation times can extend to around 10 ns and are sufficient to observe the growth of mesophases from an isotropic liquid. The results from a number of studies look very promising, and a wealth of structural and dynamic data now exists for bulk phases, monolayers and bilayers. Continued development of force fields for liquid crystals will be particularly important in the next few years, and particular emphasis must be placed on the development of all-atom force fields that are able to reproduce liquid phase densities for small molecules. Without these it will be difficult to obtain accurate phase transition temperatures. It will also be necessary to extend atomistic models to several thousand molecules to remove major system size effects which are present in all current work. This will be greatly facilitated by modern parallel simulation methods that allow molecular dynamics simulations to be carried out in parallel on multi-processor systems [115]. 

Jorgensen, W. L., Maxwell, D. S., Tirado-Rives, J. Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids. J. Am. Chem. Soc. 

In all cases the calculations were performed using QM/MM methodology that includes the pseudobond model for the QM/MM boundary [13,39,41]. This methodology has been implemented in a modified version of Gaussian 98 [42], which interfaces to a modified version of TINKER [43], The AMBER94 all-atom force field parameter set [44] and the TIP3P [45] model for water were used. 

Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids. 

Cui et al. performed similar analyses to fhose of Dupuis and co-workers. The side chain-side chain radial disfribufion functions (RDFs) reported by Cui et al. show remarkable qualitative deviation from fhose in Zhou et al. i It is of note that the united atom approach used by Cui and co-workers ignored electrostatic interactions between CP2 groups of the polymeric backbone. This can lead to a poor description of fhe hydrated structure in the regions close to the polymeric backbones, unlike the all-atom force field used in Zhou et al. ° For the sake of limited computational resources, Cui et al. used a relatively short representation of Nation ionomer chains consisting of three monomers as compared to the ten monomers used by Vishnyakov and Neimark or Urata et al. It can be expected that structural correlations will strongly depend on this choice. 

Jorgensen, W. L. and McDonald, N. A. (1998) Development of an all-atom force field for heterocycles. Properties of liquid pyridine and diazenes../. Mol. Struct. (Theochem.) 424, 145-155. 

T. Herges and W. Wenzel. Reproducible in-silico folding of a three-helix protein in a transferable all-atom force field. Physical Review Letters (in press), http //www.arXiv.org physics/0310146, 2004. 

T. Herges and W. Wenzel. An All-Atom Force Field for Tertiary Structure Prediction of Helical Proteins. Biophys. J., 87(5) 3100-3109, 2004. 

A. Schug, T. Herges, and W. Wenzel. All-atom folding of the trp-cage protein in an all-atom force field. Europhyics Lett., 67 307-313, 2004. 

Canongia Lopes, J.N., Deschamps, J., and Padua, A.A.H., Modeling ionic liquids using a systematic all-atom force field, /. Phys. Chem. B, 108, 2038-2047,... 

In these models, the potential energy function is based on the molecular mechanics all-atom force field and includes the bond, angle, dihedral and non-bonded energy terms. The parameterization is based on the statistical analysis of sets of experimental structures. If a variable q describes a degree of freedom in the system (e.g., bond distances, angles, dihedrals) then, P(q), the probability distribution associated with this degree of freedom, is related to the potential of mean force, W(q), by the following equation... 

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