Faculty for Chemistry and Pharmacy - Group of Prof. Zipse
 

GaussView

The program GaussView 3.0 by Gaussian Inc. is a tool for inspecting the input and output files generated by Gaussian 03. Earlier versions of GaussView cannot be used with output files generated by Gaussian 03, and GaussView 3.0 will not work properly with output generated by Gaussian 98. In order to start the program type:

gv3

on the command line. After the graphical user interface appears, select "Open .. " from the "File" menu. In the resulting popup window, the files contained in a subdirectory are displayed and can be opened by double clicking. Before successfully loading a file, the appropriate file type must also be selected. If, for example, the output file test1.log should be loaded, the file type selector must be set to ".log". Gaussian 03 input files can be read as file type ".com", but this option only works reliably with input files NOT containing any information for the queueing system.

Upon loading an output file, GaussView displays the information contained in the archive entry at the end of the file. In case of a geometry optimization, the structure shown will be the final structure obtained after optimization. In case no archive entry can be found in the output file, the program will read the last structure in the file. In order to display all the structures contained in the output file select the Open option from the File menu. In the new window offering you several options for loading files select Gaussian Output File in the Open as: box, activate the Read Intermediate Geometries checkbox at the bottom of the window, and enter the name of an existing output file. After closing the window with the Open button, a new window appears displaying the last structure contained in the output file. This new window also sports a green button at the top left corner allowing you to start (and stop) the animation of all structures in the file. At the right side of the green button you can also see a small window displaying the number of the currently displayed structure in the file. When loading of the output file proceeds properly, the Results menu also allows you to select the Optimization option. This yields a new window displaying the energies as well as the RMS gradients of all structures in the output file as a 2D graph. Please observe that you can load multiple structures only from geometry optimization output files and not from output files of compound jobs (e.g. geometry optimization plus single point calculation). New input files can be generated by choosing the "Save .. " option from the "File" menu. The supported file types are those used by Gaussian 03, the mol2 file type used in Sybyl, and the mol file type used by MDL software.

New molecules can be build quickly with the options displayed on the Builder panel. Larger substructures can be accessed through the Rings and Group buttons while fragments of peptides and oligonucleotides can be found behind the button with the double helix. Single bonds and atom types can be modified with the Bond and Element buttons while bond and dihedral angles can be adjusted selectively with the Angle or Dihedral buttons.

Various results from calculations with Gaussian 03 can be accessed through the "Results" menu. Even though energies and charge distribution are better obtained directly from the output file, the results of frequency calculations or the shape of molecular orbitals can very nicely be visualized through the options "Vibrations ..." and "Surfaces ...". The vibrational frequencies can be selected from a popup window by mouseclick, and frequency as well as amplitude of the animated vibration can be set with the Frames/Cycle and Displacement rulers. The information needed for a 3D display of molecular orbitals can best be taken from the binary checkpoint file (file type ".chk") or by loading a "Cube" file specifically generated during a Gaussian run (file type ".cub").

The appearance of all plots can be changed through the appropriate options in the "View" pulldown menu, the options "Show Tags" and "Show Symbols"being the most useful in many cases.

In order to stop the program, choose "Exit" from the "File" menu.

In case nothing works: remember that most standard UNIX versions and LINUX distributions include the program "GhostView" which (in many cases by default) can also be started with the alias "gv". Older versions of GaussView can be started using the "gv2", "gaussview2", or "gaussview" commands.
 


last changes: 06.11.2007, HZ
questions & comments to: zipse@cup.uni-muenchen.de