Consistent force field potential energy function

Consistent Force Field Potential Energy Function, CFF-PEF... 

Molecular Dynamics and Monte Carlo Simulations. At the heart of the method of molecular dynamics is a simulation model consisting of potential energy functions, or force fields. Molecular dynamics calculations represent a deterministic method, ie, one based on the assumption that atoms move according to laws of Newtonian mechanics. Molecular dynamics simulations can be performed for short time-periods, eg, 50—100 picoseconds, to examine localized very high frequency motions, such as bond length distortions, or, over much longer periods of time, eg, 500—2000 ps, in order to derive equiUbrium properties. It is worthwhile to summarize what properties researchers can expect to evaluate by performing molecular simulations ... 

Vibrational spectroscopy has played a very important role in the development of potential functions for molecular mechanics studies of proteins. Force constants which appear in the energy expressions are heavily parameterized from infrared and Raman studies of small model compounds. One approach to the interpretation of vibrational spectra for biopolymers has been a harmonic analysis whereby spectra are fit by geometry and/or force constant changes. There are a number of reasons for developing other approaches. The consistent force field (CFF) type potentials used in computer simulations are meant to model the motions of the atoms over a large ranee of conformations and, implicitly temperatures, without reparameterization. It is also desirable to develop a formalism for interpreting vibrational spectra which takes into account the variation in the conformations of the chromophore and surroundings which occur due to thermal motions. 

A short presentation of the Consistent Force Field is given, with emphasis on parametrization and optimization of energy function parameters. For best possible calculation of structure, potential energy functions with parameter values optimized on both structural and other properties must be used. Results from optimization with the Consistent Force Field on alkanes and ethers are applied to glucose, gentiobiose, maltose and cellobiose. Comparison is made with earlier and with parallel work. The meaning and use of conformational maps is discussed shortly. 

In an exact representation of the interaction between a solute and a solvent, i.e., solvation, the solvent molecules must be explicitly taken into account. That is, the solvent is described on a microscopic level, where the individual solvent molecules are considered explicitly. The interaction potential between solvent molecules and between solvent molecules and the solute can, in principle, be found by solving the electronic Schrodinger equation for a system consisting of all the involved molecules. Typically, in practice, a more empirical approach is followed where the interaction potential is described by parameterized energy functions. These potential energy functions (often referred to as force fields) are typically parameterized as pairwise atom-atom interactions. 

A vast amount of empirical molecular potential energy functions and a series of corresponding programs (molecular mechanics and consistent force field programs) are available (for recent reviews see 203 205)). Unfortunately these energy functions are always the result of optimization on a rather limited group of compounds. No... 

Engelsen SB, Eabricius J, Rasmussen K (1994) The consistent force field. 1. Methods and strategies for optimization of empirical potential energy functions. Acta Chem Scand Ser A... 

Jonsdottir SO, Rasmussen K (2000) The consistent force field. Part 6 an optimized set of potential energy functions for primary amines. New J Chem 24 243-247... 

The MM method will be seen to be the most useful one for obtaining force constants that can be used for different conformations of the molecule. In this approach the force constants are obtained from the second derivatives of an assumed potential energy function consisting of quadratic bonded tenns and non-quadratic non-bonded terms. Although present MM functions are too crude to be spectroscopically reliable, a new method for deriving such functions holds the promise of providing a reliable vibrational force field for the polypeptide chain. 

The interatomic potentials define the force field parameters that contribute to the lattice energy of a relaxed or energy minimized structure. The fundamental question is how reliable is a force field The force field used in evaluating a potential function must be consistent and widely applicable to all similar systems. It must be able to predict the crystal properties as measured experimentally. Two main approaches, namely empirical and semi-empirical, are usually employed in the derivation of potential parameters. Empirical derivations involve a least square fitting routine where parameters are chosen such that the results achieve the best correlation with the observed properties. The semi-empirical approach uses an approximate formulation of the quantum mechanical calculations. An example of such an approximation is the electron gas method [57] which treats the electron density at any point as a uniform electron gas. The following is the analytical description of the potential energy function and interatomic potentials we recommend for use in simulation of zeolites and related system. 

In this study, n-hexane, n-hexadecane and cyclohexane are assumed as lubricants. The 3-D models of lubricants are shown in Figure 2. The intramolecular and intermolecular interactions are calculated using the OPLS-AA, optimized potentials for liquid simulations -all atom, force field potential [10,11]. In this force field, the potential energy function consists of harmonic bondstretching and angle-bending terms, a Fourier series for torsional energetics, and Coulomb and Lennard-Jones terms for the nonbonded interactions, as defined in eqs. (l)to(4). 

A force field is a set of force constants used in the calculation of a vibrational spectrum. In the consistent force field context, a force field is derived from a potential energy function, for a particular conformer of a molecule. The force field will be different for another conformer of the same molecule, and for another molecule. See also ref. 190, section 6.1. 

A consistent force field is conceptually rather different from a force field. It is a potential energy function whose parameters have been fitted, preferably optimised in some objective way, to reproduce structures of a set of molecules and, through the force field derived for each molecule of the set, molecular spectra. Other pro-... 

CHARMM is the first program system published which deserves the designation "molecular mechanics , in the sense that it treats static, kinematic and dynamic properties. All other programs available are much more limited in scope. A few warnings for the uninitiated are in place The more complicated a system is, and here I mean only modern well-structured and well-documented systems, the more attention is required to maintain and operate it, and that cannot be left solely to the computer people. Also, know-how does not come by itself or on a tape. For many prospective applications, potential energy function parameters, or even the functions themselves, are lacking, just as for the simpler systems. Parameters must be found by trial and error, as is usual, or, preferably, by optimisation, which cannot be done in CHARMM a program of the consistent force field family is necessary. 

The choice of Internal coordinates as an object for optimisation Is obvious use of rotational constants maybe less so. They certainly do not give very detailed Information about the conformation of a molecule, but they are the primary structural Information derived from rotational and ro-vlb spectroscopy on small molecules. The Inclusion of dipole moments Is a must when Coulomb terms are present In the potential energy function. Charges are Included, although they are not experimentally observable quantities, because It may be desirable to lock a parameter set to data derived from photoelectron spectroscopy or from ab Initio calculations with a large basis set. Quite naturally we want to optimise on vibrational spectra, and we shall see below that It Is a bit more cumbersome In the consistent force field context than In traditional normal coordinate analysis. 

All members of the consistent force field family of programs are available, from QCPE or from the authors they are described under section 3.4 They are all singular in a way they allow for optimisation of potential energy function parameters on many types of observable, and are therefore splendid tools in the hands of a skilled worker. 

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