Default force field

In Sections 17.11-17.14, we will manipulate the force field. Momec3 has a built-in standard force field that can be restored in the project-systems-system-forcejields section by using the defaults option. One can either modify the existing force field, and restore it to the default force field later or add an (empty) force field and set it to the Momec3 default by pressing default When you work on a copy of the force field, remember to select the correct force field when submitting jobs via calc-queue-add. 

Atom types represen t the chemical environment of an atom. The atom types associated with a given force field could be hard-wired to have specific vahiesand meaning. llyperChem also allows flexible definitions of the atom types and the associated chemical en vironmen Is. Th e ch em ical en viron men t of an atom (a set of rules for defining a type) and the default rules are in a standard ASCII text file, chem.nil. included with llyperChem. You can modify this file and compile it m a binary form that llyperChem... 

The default parameters for bond stretching are an ec iiilibriiim bond length an d a stretch in g force eon starit. fb e fun etion al form isjiist that of the. M.M+ force field including a correction for cubic stretches. The default force constant depends only on the bond... 

I h e -M. l+ force field assigns default values for out of plane bending terms around an sp2 center. If a central atom has some out of plane parameters, then the first out of plane parameter involving th at cen tral atom is used if a specific parameter is n ot foiin d. 

Chem comes with default parameter sets, Amber2 and Amber3 in the case of the AMBER method. It is possible, however, to define an arbitrary number of additional parameter sets for the AMBER method (or for any of the other three force field methods). These user-defined parameter sets can be specified in the Parameters dialog box and integrated into HyperChem, in the same way as the default sets. 

In computational chemistry it can be very useful to have a generic model that you can apply to any situation. Even if less accurate, such a computational tool is very useful for comparing results between molecules and certainly lowers the level of pain in using a model from one that almost always fails. The MM+ force field is meant to apply to general organic chemistry more than the other force fields of HyperChem, which really focus on proteins and nucleic acids. HyperChem includes a default scheme such that when MM+ fails to find a force constant (more generally, force field parameter), HyperChem substitutes a default value. This occurs universally with the periodic table so all conceivable molecules will allow computations. Whether or not the results of such a calculation are realistic can only be determined by close examination of the default parameters and the particular molecular situation. ... 

There are some systems for which the default optimization procedure may not succeed on its own. A common problem with many difficult cases is that the force constants estimated by the optimization procedure differ substantially from the actual values. By default, a geometry optimization starts with an initial guess for the second derivative matrix derived from a simple valence force field. The approximate matrix is improved at each step of the optimization using the computed first derivatives. 

Molecular Mechanics Features ChemSite performs energy minimization and molecular dynamics simulation. Available force fields include Amber, mm2 and the ChemSite s default cm+ force field for accurate calculations with almost any molecule. The program performs real time animation of energy minimization and molecular dynamics simulation with small to medium size molecules. With large molecules such as proteins, movies of molecular dynamics simulations may be recorded to disk and played back for real time animation. 

MOMEC also allows single point calculations, i. e., there will be no structural optimization after the calculation of the strain energy. The result of this calculation depends (i) on the structure that you have generated, (ii) on the functional forms of the terms in the above equations and (iii) on the parameters used in these functions. The latter two together define the force field, and this is easily modified in MOMEC. For the moment, we do not address this aspect and carry out our calculations with the default set of functions and parameters provided. 

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