AMBER functional form

Soon after this initial study, several other groups developed force fields for imidazolium-based ionic liquids. Stassen and coworkers [83] reported a force field for [EMIM][A1C14] based on the so-called AMBER functional form. This functional form is widely used in the simulation of organics and is given by... 

We finish the discussion of force fields developed for imidazolium-based systems by describing the work of Voth and co-workers who simulated [C2mim][N03] first with traditional fixed-charge models and then with a model that included electronic polarizability. For the fixed-charge system, Del Popolo and Voth used a force field having the AMBER function form, with parameters for the cation and anion taken from existing sources. They... 

Hach molecular mechanics method has its own functional form MM+. AMBER, OPL.S, and BIO+. The functional form describes the an alytic form of each of th e term s in th e poteri tial. For exam pie, MM+h as both a quadratic and a cubic stretch term in th e poten tial whereas AMBER, OPES, and BIO+ have only c nadratic stretch term s, I h e functional form is referred to here as the force field. For exam pie, th e fun ction al form of a qu adratic stretch with force constant K, and equilibrium distance i q is ... 

In principle, atom types eoiild be assoeiated wilh a partieiilar parameter set rather than the functional form or force field. In HyperChern, however, atoms types are rigorously lied to a force field . M.M-t, AMBER, OPTS, and BIO+. Each of the force fields has a... 

The fiinctioiial form for electrostatic in teraction s m AMBER is identical with that shown in equation (2fi) on page 179. You normally use a dielectric scaling of D=1 with AMBER com bin ed with a constant functional form when solvent molecules are explicitly... 

The functional form for bond stretching in AMBER is quadratic only and is identical to that shown in equation (11) on page 175. The bond stretching force constants are in units of kcal/mol per A and are in the file pointed to by the QuadraticStretch entry for the parameter set in the Registry or the chem.ini file, usually called =>istr.txt(dbf). 

The functional form for angle bending in AMBER is quadratic only and is identical with that shown in equation (12) on page 175. The... 

The functional form for van der Waals interactions in AMBER is identical with that shown in equation (13) on page 175. The coefficients A. and B.. are computed from the parameters in the file pointed to by the 6-12AtomVDW entry for the parameter set in the Registry or the chem. ini file, usually called nbd.txt(dbf), and optionally with the file pointed to by the 6-12PairVDW entry for the parameter set, usually called npr.txt(dbf). The standard AMBER parameter sets use equations (15) and (16) for the combination rules by setting the 6-12AtomVDWFormat entry to RStarEpsilon. The 1 van der Waals interactions are usually scaled in AMBER to half their nominal value (a scale factor of 0.5 in the Force Field Options dialog box). 

Amolecular mechanics method in HyperChem is defined by a set of atom types and a functional form for the energy and its derivatives— for example AMBER. For the AMBER method, you may use many different default and user-defined parameter sets. Hyper-... 

MM methods provide a simpler representation of molecules, in which the fine detail of the electrons represented implicitly via partial charges and, is some cases, molecular polarisabilities. MM models represent molecules as a collection of atoms interacting through classical potentials. There are several MM models (or forcefields), and they dilfer in the functional forms of the interaction potential used between atoms, and in the means by which these interaction potentials are parameterized. Several good recent reviews of MM forcefields have been produced. Several MM forcefields have been developed for application to biomolecular systems. The most popular of these are the CHARMM, AMBER, ... 

The functional form of Emm is the same as in Galaxy and AMBER (version... 

Standard molecular mechanics (MM) methods (e.g. the popular force fields developed for AMBER, CHARMM and GROMOS decribed in Section 2 above) provide a good description of protein structure and dynamics, but cannot be used to model chemical reactions. This limitation is due their simple functional forms (e.g. harmonic terms for bond stretching) and inability to model changes in electronic polarization (because of the invariant point partial atomic charge used by these molecular mechanics methods to represent electrostatic interactions). 

The potential functions used in the simulation of biological molecules contain terms involving bond stretching, bond angle, and torsional motions along with nonbond and electrostatic interactions. - jhe functional form of the AMBER total potential is given in Eq. [17]. 

We now discuss in some detail the individual contributions to a molecular mechanics force field, giving a selection of the various functional forms that are in common use. We shall then consider the important task of parametrisation, in which values for the many force constants are derived. Our discussion will be illuminated by examples chosen from contemporary force fields in widespread use and the MM2/MM3/MM4 and AMBER force fields in particular. 

Force fields for [BMIM][PF6] that explicitly treat aU hydrogens (all-atom models) were developed soon after this by Margulis et al. [14], and Morrow and Maginn [11], while Stassen and coworkers [83] published a force field for the [EMIM]+ and [BMIM]+ cations paired with tetrachloroaluminate and tetrafluoroborate anions. The force fields aU have similar functional forms, and parameters were again maiiily developed using literature force field parameters for similar compounds and ab initio calculations of single ions or ion pairs. In these and later studies, repulsion-dispersion parameters were generally adapted from those available from one of three popular force field databases (Amber [114], OPLS [118] and CHARMM [119]). For [BMIM][PF6], the added realism of the all-atom model enabled densities to be predicted vyithin 1% of the experimental value [11]. The first indications of restricted dynamics in these systems were also observed [11,14,15]. 

The total LFMM energy is, therefore, calculated from an electronic term (LFSE) and additional terms that can be obtained from a conventional force field, such as AMBER [3], CHARMM [4], or the more complex MMFF [36]. Caution is needed when handling the energy terms involving metal atoms, such as the explicit metal-ligand bond energy Em l- The functional forms may need to be adjusted and parameters refitted to lead to correct coordination geometries. For example, Em-l is better described by a Morse function... 

Lennard-Jones potentials. Because it is not our intention to review all advantages and applications of these different functional forms and parameter sets, we shall focus our explanations to the well-known AMBER force field (2, 3). This parameter set is widely used, and has already been successfully applied to molecular dynamics simulations of various surfactant systems. 

DL POLY. DL POLY is a parallel molecular dynamics simulation package originally developed at the Daresbury Laboratory in England. Parameters for the current DL POLY 3 force field may be obtained from the GRO-MOS, AMBER, and DREIDING force fields that share functional forms. 

The kind of energy terms, their functional form, and how carefully (number, quality, and kind of reference data) the parameters were derived determine the quality of a force field. Accurate force fields exist for organic molecules (e.g., MM2, MM3), but more approximate force fields (e.g., with fixed bond distances) optimized for computational speed rather than accuracy [e.g., AMBER (assisted model building with energy refinement), CHARMM (chemistry at Harvard molecular mechanics), GROMOS (Groningen molecular simulation)] are the only practical choice for the treatment of large biomolecules. The type of molecular system to be smdied determines the choice of the force field. 

The term "AMBER force field" generally refers to the functional form used by the family of AMBER force fields. This form includes a number of parameters each member of the family of AMBER force fields provides values for these parameters and has its own name. The functional form of the AMBER force field is (equation 8.1). 

Two well-established computer programs for MD simulations are CHARMM [24] and AMBER [219], which implement a similar functional form of the atomistic force field and include a large number of tools for setting up the files required to run an MD simuIatiOTi. 

---