Dialogs, settings

Output from the search process is a fully compatible Dialog set, thus the output of a query search (QS) may be combined with the output from a text search or... 

Be careful when you use the Orbital Criterion for symmetrical system s. To get correct resnlis, you in u st include all or none of any set of degenerate orbitals in the Cl, n ot jn si some of them. Carrying out an RIIF calculation first and studying the Orbitals dialog box will help you to spot degenerate orbitals and avoid this pitfall. 

Run a molecular dynamics simulation, Start another simulation with the same molecular system and with Restart off in the Molecular Dynamics dialog box. HyperCheni assigns a new set of velocities at random. ... 

You can restrain atom s dur ing m olecu lar m ecli an ics or quart tu in mceh an ies calculation s, Cli oosiri g restrain ts, via the Restrain t Horces dialog box, applies additional h arm on ie forces which you specify, to in teratorn re distari CCS, an gles, or dihedrals that you have set up as named selections. 

After you select a method for a semi-empirical calculation (using the Semi-empirical item on the Setup menu l, choose Optionsm the dialog box to set conditions for the calculation. You sec the Semi-empirical Options dialog box. Th e I ollowmg section s explain th esc option s. 

HyperChem run s the molecular dynain ics trajectory, averaging and analyzing a trajectory and creating the Cartesian coordinates and velocities, fhe period for reporting these coordinates and velocities is th e data collection period. At-2. It is a m iiltiplc of the basic time step. At = ii At], and is also referred to as a data step. The value 1I2 is set in the Molecular Dynamics options dialog box. 

Coordin ates of atom s can he set by n orm al translation orrotation of HyperCh cm molecules, fo set initial velocities, however, it is necessary to edit th e H l. file explicitly. The tin it o f velocity in the HIN file is. An gstrom s/picosecon d.. Areact.hin file and a script react.scr are in eluded with HyperChem to illustrate one simple reacting trajectory. In order to have these initial velocities used in a trajectory the Restart check box of the Molecular Dynamics Option s dialog box must he checked. If it is n ot, the in itial velocities in the HIN file will be ignored and a re-equilibration to the tern peratiire f of th e Molecular Dyn am ics Option s dialog box will occur. This destroys any imposed initial conditions on the molecular dynamics trajectory. 

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). 

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. 

For geometry optimizations and comparison of total energies (which should be carried out with ZINDO/1, not ZINDO/S), both overlap weighting factors (Sigma-Sigma and Pi-Pi) should be set to 1 in the Semi-empirical Options dialog box. 

For constant temperature dynamics where the constant temperature check box in the Molecular Dynamics Options dialog box is checked, the energy will not remain constant but will fluctuate as energy is exchanged with the bath. The temperature, depending on the value set for the relaxation constant, will approach con-stan cy. 

To create a set of snapshots of any molecular dynamics run, press the Snapshot button of the Molecular Dynamics Options dialog box to bring up the Molecular Dynamics Snapshots dialog box for naming a snapshot file. A snapshot file contains snapshots of the coordinates and velocities of a molecular system along the trajectory. The dialog box allows you to name the file and decide at what frequency to take snapshots. For example, choosing the snapshot period to be two data steps implies that only every other time step is stored in the snapshot file. 

A family data set is a grouping of models and data for a problem (plant or system). To select a family, from the File menu choose Select Database. The Select Family dialog appears with the name of the currently selected family in the title bar. Choose the desired family from the list by double-clicking" the name. A pop-up menu appears from which the following options may be... 

If Modify is chosen from the menu, a drop-down menu with the available data types appears Family, Event " ees, Systems, End States, Basic Events, Attributes, Analysis Types, Gates, Hi rams, P Ls, Change Sets, and Flag Sets. After selecting an option, a dialog containing a li f of all records for the selected data type appears. The functions Add, Copy, Modify, and C be selected from another pop-up menu. 

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