Pseudo-force field

Once the basic suggestions are made then a pseudo-force field is used to optimize the structures. This force field contains several simplifying assumptions, which help to make this a very rapid computation. Among other things, the force field optimization is only applied to ring system. Acyclic portions are simply treated according to a so-called principle... 

ICM [64] pseudo-Brownian sampling and local minimization mbced force field and empirical score... 

Some force fields use the so-called united atom approach where (for example) a methyl group is treated as a single pseudo-atom. They arose historically in order to save computer resource when dealing with large systems such as amino-acid chains. 

Pseudo-Newton-Raphson methods have traditionally been the preferred algorithms with ab initio wave function. The interpolation methods tend to have a somewhat poor convergence characteristic, requiring many function and gradient evaluations, and have consequently primarily been used in connection with semi-empirical and force field methods. 

The MM2 force field3 is probably the most extensively parameterized and intensively used force field to date. It reproduces a variety of molecular properties such as geometry, dipole moments, conformational energies, barriers to rotation and heats of formation. Of particular importance for calculations of amines is that MM2 treats lone pairs on sp3 nitrogens (and oxygens) as pseudo atoms with a special atom type and parameters. A closely related force field, MM2 7, was derived from MM2 by Osawa and Jaime. MM2 uses the same potential functions as MM2, but employs a different set of parameters in an attempt to better reproduce barriers to rotation about single C—C bonds. 

By the use of other assumptions, the thermodynamic treatment can be simplified and more progress can be made. In particular. Hill has shown that a system of considerable utility can be obtained by considering the adsorption process as a pseudo one-component system. Only the adsorbate is considered as taking an active part. The adsorbent is assumed inert and the only effect of its presence is that its surface provides an attractive force field for the adsorbate molecules. 

In the case of BPA-PC [51], the chosen microstructures had cube-edge lengths of 18.44 A and a degree of polymerisation of 35 (Mw = 4532). There are 485 atoms or atom groups in each cube (methyl groups are represented as spherical pseudo-atoms). The force field [46] has fixed bond lengths and fixed... 

As described in the Introduction, it is usually possible to consider the modeling of experimental data separately from the scheme actually used to move atoms about. Ideally, the different models should be able to be used in the different minimization or dynamics schemes. Thus, the subsequent sections describe the kind of data offered by NMR and the kinds of penalty functions or pseudo-energy terms that can be used to represent them. For convenience, we use nomenclature common to force field-based approaches where one refers to a distance constraint potential Vdc r) as a function of intemudear distance. 

A more difficult question is the relative balance between the conventional force field and the pseudo-energy terms representing experimental data.81 If... 

The calculation of the energy or the fitting of the test sequence in the fold of the template is no easy matter. The utilization of a full force field with complete atom representation does not properly discriminate between the different folds [31]. This seems to be related to an energy surface that is too fine and the presence of numerous local minima. In its place a potential function based on a statistical analysis of known protein structures has been developed [34], The pair-wise penalty function provides a pseudo-energy based on the number of times the specific interaction has been observed in known protein structures. This function provides amino acid-amino acid interactions as well as a measure for the solvent exposure of each amino acid [34],... 

Molecular force fields and chemical shift pseudo-forces 75... 

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