Mod:gv basic
Basic GaussView Tutorial
Getting to grips with GaussView, building large molecules, and submitting Gaussian jobs from Windows.
Building a Molecule
To start GaussView, click on the Start button at the bottom left hand side of the screen. Select Programs, and then GaussView.
When GaussView is launched, three windows should appear. The first contains the welcome message which should disappear automatically. The second is the main GaussView window (grey) and the third is the Builder window (blue). WARNING: clicking anywhere in the blue space normally causes the program to build whatever fragment is selected in the grey panel. Therefore if you need to select this panel, you must click around the edge of the window, not in the centre of the panel.
The grey panel has several buttons on the bar at the top. In order to see what each button does, you can place the mouse over it and the description will appear at the bottom of the panel.
Here are instructions on how to use the mouse button and keyboard to manipulate your molecule:
| Modifiers + Mouse Button: | Action: | Condition: | Function: |
|---|---|---|---|
| Left | Click | Atom or fragment shown in GaussView window (grey) | Insert atom or fragment |
| Left | Click | Action button selected in GaussView window (grey) | Apply action |
| C + Left | Click | Select or deselect atom | |
| R + Left | Drag | Select or deselect atoms with 'rubberband' | |
| Left | Drag Up/Down | Rotate about X axis | |
| Left | Drag Left/Right | Rotate about Y axis | |
| Shift + Left | Drag | Translate molecule in XY plane | |
| Right | Drag Up/Down | Zoom Out/In | |
| Right | Drag Left/Right | Rotate about Z axis | |
| Right | Click | Open context menu | |
| If two or more fragments are not connected by bonds, actions in bold can be applied to them individually if the Alt key is pressed. The fragment closest to the cursor is affected. For example, Alt + Shift + Drag will translate one fragment independently of another. | |||
If you experience any problems, click on the Help menu in GaussView or ask one of the demonstrators for help and assistance.
(1) To start with, you will want to build a molecule so you need to select one of the ‘fragment’ buttons on the left hand side of the bar. Notice that initially the tetrahedral C fragment is selected and this is shown in the grey panel and written on the button in the centre. If you want to draw a naphthalene molecule, for example, click on the Ring Fragment button. A benzene molecule will appear in the grey window. Click on the benzene button (or you can click on the Ring Fragment button again) and choose naphthalene. You will notice that the button in the centre of the grey panel has now changed to ‘naphthalene’ and the picture in the panel has also changed accordingly. Now click in the blue panel and your structure will appear. If you would like to open a new Builder Window (blue), select File → New → Create MolGroup.
(2) By selecting different fragments you may add other groups to the structure. You can also modify the structure using the Modify Bond, Modify Angle and Modify Dihedral buttons. There are also buttons that allow you to add valences to atoms and to delete atoms. The Clean option (under the Edit menu) is useful for cleaning up structures that are far from their equilibrium positions.
(3) Go to the Ring Fragment panel and select the chair conformer of cyclohexane. Now try modifying the structure to generate the boat conformer.
(4) You can now practice using GaussView by drawing some simple molecules of your choice.
Launching a Gaussian09 calculation
Once you have built your cyclohexane boat conformer, you are ready to set up a Gaussian input file and run a calculation.
[PLEASE NOTE THAT YOU CAN RUN ONLY ONE JOB AT A TIME INTERACTIVELY USING THE WINDOWS VERSION OF GAUSSIAN.]
(1) Go to the Calculate menu and select Gaussian.
(2) A window will appear with several different menus to allow you to set up a range of different calculations. You can choose the type of calculation you want to run under the Job Type menu, and you may also want to change the method, basis set, charge or multiplicity under the Method menu. For this exercise, set up a geometry optimization using a semi-empirical method at the AM1 level.
[The memory (%mem) is set to 6MW by default. Do not exceed the total amount of memory of the laptop in any of the jobs you run. A reasonable value for %mem would be 250MB.]
(3) Once the calculation has been set up correctly, click on the Submit button at the bottom of the window.
(4) You will be prompted to save an input file. Type the name of the file (e.g. cyclohexane) in the box at the bottom. The program will save the file as a .gjf file by default which is the file type needed to run the Gaussian job via GaussView. Do not save the input file with suffix other than .gjf as GaussView will not recognise this. Other extensions such as .com or .inp works fine in other versions of Gaussian. Before you click Save, make sure your files are written to the C:\G03W\Scratch directory. You may need to go up a directory in the tree to find this.
(5) Once you click Save your job will be launched automatically using the Windows PC version of Gaussian - G03W. To follow the progress of your job, click on the Gaussian 03 button at the bottom of the screen. The job will take a little time to complete. While it is running, you might like to try out some of the GaussView tutorials on the Gaussian web site.
Visualizing the results
(1) Once the job has finished, you will be asked if you would like to close the Gaussian window. Click Yes. You will then be asked if you want to view the results file. Again click Yes, and select file type Gaussian Output Files and identify the relevant .log file from the list. At this point, you also have the option to read in the intermediate geometries by checking the box at the bottom. Check the Read Intermediate Geometries box and click Open.
(2) A new blue window should appear and you can step through the intermediate geometries or animate them by clicking on the green button.
(3) You can view other information about the job by going to the Results menu. Summary gives a summary of the final results obtained, and Optimization illustrates the convergence of the energy and gradient during the optimization. You also have the option to view the whole log file by selecting View File.
(4) In some cases it may be necessary to read information from the checkpoint file (chk) rather than the log file (e.g. to plot up orbitals) [more later in Practical session 2]. This file can also be used to restart jobs. This file is written by default and is named according to the name of your input file. The name and location of this file can be changed manually under the Link 0 menu in the Gaussian calculation setup. If you do not specify a location for the chk file, it will be written to the C:\G03W\Scratch directory and you can retrieve it from there. Open the chk file corresponding to the cyclohexane optimization. Select Open under the File menu, choose file type Gaussian Checkpoint Files (*.chk), identify the relevant chk file and click Open.