Setting Up Options

Semi-empirical methods could thus treat the receptor portion of a single protein molecule as a quantum mechanical region but ab mdio methods cannot. However, both semi-empirical and ab initio methods could treat solvents as a perturbation on a quantum mechanical solute. In the future, HyperChem may have an algorithm for correctly treating the boundary between a classical region and an ab mdio quantum mechanical region in the same molecule. For the time being it does not. 

Certain options are needed to setup for running quantum mechanics calculations in HyperChem via the corresponding option dialog boxes on the Setup menu. 

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MSBACKUP A DOS program that allows the user to make backup copies of all the programs and data stored on the hard disk. This program is menu-driven and allows the user to set up options that can be used each time you back up the hard drive. 

Setup pages (middle part of the screen) that contain all the set-up options. 

PC Model has some features that are not found in many other molecular mechanics programs. This is one of the few programs that outputs the energy given by the force field and the heat of formation and a strain energy. Atom types for describing transition structures in the MMX force field are included. There is a metal coordination option for setting up calculations with metal atoms. There are also molecular similarity and conformation search functions. 

GaussView (we used Version 2.08) is a graphic interface for use with the Gaussian ah initio program. It can be used to build molecules, set up the options in the input hie, run a calculation, and display results. GaussView uses the molecule builder that was written by SemiChem, but has screens for setting up calculations that are different from those in the AMPAC GUI sold by SemiChem. 

Commercial computer computation services are being set up to provide shortcut calculation options. These provide considerable savings for preliminary design studies. 

Benzene will dearly illustrate this effect. Compare the first six excited states, as predicted using the 6-31G and 6-31-t-G basis sets. When setting up the route section for these jobs, include the NSfate =8 option. Although we are only looking for six... 

Nonisothermal reactors with adiabatic beds. Optimization of the temperature profile described above assumes that heat can be added or removed wherever required and at whatever rate required so that the optimal temperature profile can be achieved. A superstructure can be set up to examine design options involving adiabatic reaction sections. Figure 7.12 shows a superstructure for a reactor with adiabatic sections912 that allows heat to be transferred indirectly or directly through intermediate feed injection. 

Consider now ways in which the best arrangement of a distillation sequence can be determined more systematically. Given the possibilities for changing the sequence of simple columns or the introduction of prefractionators, side-strippers, side-rectifiers and fully thermally coupled arrangements, the problem is complex with many structural options. The problem can be addressed using the optimization of a superstructure. As discussed in Chapter 1, this approach starts by setting up a grand flowsheet in which all structural features for an optimal solution are embedded. 

We have added a companion option to PBUILD, PRANDOM which eases considerably the problem of finding good conformations of a polymer segment. PRANDOM automatically selects all of the polymer backbone and/or side chain bonds and will randomly select rotations for each bond. In a few minutes, one can not only build a polymer fragment, but also set up a Monte-Carlo search of its conformational space. However, even this cannot solve the problems for large models (pentamer or larger), again due to the number of bonds to be rotated. 

To set up an experiment, the researcher defines the fluid composition and Instrument control parameters. For some instruments, such as the rotational coaxial viscometers, the experiment setup can be quite complicated. For this reason, all data entry is of the fill-in-the-blank" nature. The researcher also has the option of using the experiment setup from a previous experiment for default parameters. 

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