Carlier Group Gaussian User Manual - Virginia Tech

Carlier Group Gaussian User Manual 29
b)change the suffix to get rid of the periods (you can name it anything unique!)
mv molden4.8.macosX molden4_8_osX
3. Now from the terminal window type
open molden4_8_osX
This will launch Molden. In addition to the xterm window, you will get a MOLDEN
window (blank) and a Molden Control window.
4. To open a g09 output file it must be on your computer (i.e. downloaded from
Inferno): In the Molden Control window, under Miscellaneous, click read. This will
open the Molden File Select window.
You will need to navigate to the directory that has your file. You should probably be
starting from your home directory, then type /directory/subdirectory etc to get to the
directory you want. Then select the file from the window, scrolling if necessary. Your
structure should appear in the MOLDEN window.
Note that Molden reads all the intermediate geometries, and by default, shows the
starting geometry. To see the final geometry, click the "Movie" button and you will see
all the structures move past. Alternatively you can use the "First" and "Next" buttons.
Particularly useful is the graphical presentation of Geometric convergence. Click on
the "Geom. Conv." button and you will get three graphs. Click on any point on the
Energy vs. point graph and that will take you to the corresponding structure.
Note that Molden provides a convenient method to measure distances, angles, and
dihedrals. You click on the button, then once in the structure window, and then click on
the atoms you are interested in.
You may wish to de-select the Shade box under Draw Mode in the Molden Control
window. With your cursor in the MOLDEN window you can now rotate your structure to
the desired view.
5. To see the course of the optimization on the energies, click Geom. conv. under
Convergence (Molden Control). You will get a new window called Geom.
Convergence. This is an interactive plot-click anywhere and you will go to that
structure.
6. To see the Frequencies, click the Norm. Mode box under Frequencies in the
Molden Control window. This will give you two new windows, Spectrum and Molden
Frequency Select.