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Job tools menu (left-bottom)
Save
scan animation
This item is used to create animated gif files from a scan job or a
trajectory file. If the job node is
not visible for your file, you should choose "Tools/Create
animation/Scan animation" item from the main menu; Save scan steps as multiple xyz files For scan jobs, each scan step can be saved as an individual section in .xyz file with multiple structures; Clear all bonds extracted from the file When an output file (e.g. Gamess) is read, it can contain bond computed by e.g. mulliken population analysis. Sometimes these bonds are quite improper, and to get rid of them, this menu item can be chosen; Show scanned parameter on image If you have a relaxed PES scan, you can visualize the scanned parameter (distance, angle or dihedral) with this option; Show internal parameters used in optimization When Gaussian performs a geometry optimization and the molecular geometry is specified in Cartesian coordinates, Gaussian chooses its own set of internal parameters which are optimized (unless you choose # OPT(CART)). You can use this option to check, whether these parameters have been chosen by Gaussian correctly (if not, probably you should use your own set of internal parameters to speed up the optimization); Find frequencies in which the selected atoms are mostly involved Here you can check in which frequencies the motion of selected atoms appears mostly; Compute entropy and Gibbs energy without low frequencies With this option you can compute entropy setting some threshold of small frequencies (to minimize the error cases by the anharmonicities of small frequencies). You can read more information about this feature at this webpage; Calculate frequencies by Hessian If you have opened a file with Hessian (Gaussian .fch or Orca .hess file), with this option you can compute the frequencies (this feature can mostly useful for computing the isotopic substitution effects). More information about this feature can be read at this webpage; Trajectory analysis tools These subitems can be useful for processing and visualizing trajectories (e.g. of geometry optimization). In particular, the menu subitem "Set common orientation for all geometries" can be useful, if your molecule often turns over while you brose the optimization steps:
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