Avogadro/C4/File-Extensions/English-timed

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Time
Narration
00:01 Welcome to this tutorial on File Extensions.
00:05 In this tutorial, we will learn to, Prepare input files for computational chemistry programmes such as:
GAMESS, Gaussian, MOPAC, NWChem etc.
00:18 And view Molecular orbitals and calculated IR spectrum using output files generated from: GAMESS and Gaussian software.
00:28 Here I am using Ubuntu Linux OS version. 14.04.

Avogadro version 1.1.1.

00:38 To follow this tutorial you should be familiar with, Avogadro interface.
00:43 If not, for relevant tutorials, please visit our website.
00:49 The example files required for this tutorial are provided as code files.
00:55 Please download and save them in a folder on desktop.
01:00 Here I have opened the Avogadro window.
01:04 Load a benzene molecule from Build menu using Insert fragment library.
01:12 Optimize the geometry using Auto-optimization tool from the tool bar.
01:20 Click on the Extensions menu.
01:23 Using Avogadro we can prepare input files for popular quantum codes such as:

GAMESS

Gaussian

MOLPRO

MOPAC

Q-CHEM etc.

01:36 Click on Gaussian option.A graphical data input dialog box opens.
01:43 Let me demonstrate how to generate input file for Gaussian program.
01:49 We need to fill in the required features shown in the dialog box.
01:55 Avogadro by itself cannot calculate molecular orbitals.
01:59 So let us create an Input file to view the molecular orbitals of benzene molecule.
02:05 In Gaussian input dialog box , type the title as Benzene hyphen MO.
02:11 Choose Frequencies from the Calculation drop down.

Processors as 1.

Theory as B3LYP.

6-31G(d) as Basis set.

Charge zero.

Multiplicity 1.

Output as Standard.

Format as cartesian

Check the checkpoint check box.

02:40 You can see the preview of the input file at the bottom of the dialog box.
02:45 It will be updated as you change the options.
02:49 Click on Generate button.
02:52 A Save input Deck dialog box opens.
02:56 The Gaussian input file generated will be saved with a dot com extension .
03:02 Type the file name as Benzene. Choose the location as Desktop. Click on Save button.
03:10 The file will be saved as Benzene.com on the desktop. Open the file with gedit.
03:18 Now this file can be used as an input file for the Gaussian software programme.
03: 24 About Gaussian software.
03:28 Gaussian is a computer programme for computational chemistry.
03:32 It is a commercial software developed and licensed by Gaussian Inc.

More information is available at the given link. http://www.gaussian.com/

03:41 Back to Avogadro window. Close the dialog box.
03:46 Now let us see how to prepare an input file for GAMESS programme.
03:51 Open a new window. Click on “New” from the Tools menu.
03:56 Build a water molecule using Draw tool. Change the element to Oxygen.
04:01 Click on the panel. Optimize the geometry using auto-optimization tool.
04:08 Click on Extensions menu. Select GAMESS, Input generator from the sub-menu.
04:16 A GAMESS input dialog box opens. There are two tabs Basic setup and Advanced setup.
04:24 As we did with the Gaussian input file, fill in the required information.
04:29 Under Basic Setup, we will select Equilibrium Geometry under Calculate field.
04:36 RHF, Restricted Hartee Fock method of approximation for the determination of wave function.
04:44 Since water is a small molecule, we will select 6-31G(d,p) as Basis set.
04:52 In gas phase, singlet , because all the electrons are paired.
04:58 Water is a neutral molecule, so charge will be neutral.
05:02 Click on Advanced Setup to add some more parameters to control the optimization.
05:08 Click on Basis if you want to change the set of functions.
05:12 Click on Data.
05:14 Type the Title as water-MO.
05:18 Change the Point Group to CnV.
05:21 Order of Principal Axis to 2.
05:24 For now we will keep the default parameters as such.
05:29 Click on Generate. A Save Input deck opens.
05:34 By default, the file extension is dot inp.
05:38 Type the file name as Water.
05:42 Choose the file location as Desktop. Click on Save button.
05:48 The GAMESS input file is saved as Water.inp on the Desktop.
05:55 About GAMESS
05:57 GAMESS stands for: General Atomic and Molecular Electronic Structure System.

(GAMESS)It is a general ab initio quantum chemistry package.

06:08 It is available at no cost to both academic and industrial users.
06:14 Information about installation and download is given at the following link. http://www.msg.ameslab.gov/gamess/download.html
06:20 Now we have generated input files for GAMESS and Gaussian programmes.
06:26 These input files are ready to be loaded into respective programmes.
06:31 Viewers please note: Gaussian is a commercial software. Hence I will not be able to show the interface to load the input file.
06:41 As mentioned earlier GAMESS is free software.
06:45 Those interested can download GAMESS software from the given link.

And load the input file to generate the output file. http://www.msg.ameslab.gov/gamess/download.htm

06:53 I have some Gaussian and GAMESS output files on the desktop.
06:58 I have provided these files as code files along with this tutorial.
07:03 Lets view these output files in avogadro.
07:07 Open a new Avogadro window.
07:10 Click on open icon in the tool bar.
07:13 Navigate to the file location. Select Benzene.log
07:18 The file opens, we can see the structure of benzene on the panel.
07:24 Benzene.log was generated using Gaussian.
07:28 It contains information about molecular orbitals and C-C and C-H bond stretching.
07:36 Sometimes the log file may not show orbital information.
07:40 In such case open the .fchk file provided in the codefiles.
07:47 To view the orbitals, click on the orbital name from the list.
07:54 If you want to change the display of orbitals....

Click on the spanner symbol next to surfaces option in the display types.

08:02 In the Surface Setting dialog box.Drag the slider to change the opacity. Observe the panel.
08:10 There are three options in the Render drop-down, fill, lines and points.
08:17 By default the orbitals are rendered as fill.
08:21 There is also an option to change the color of the lobes.
08:25 Click on the Color tabs next to positive and negative option.
08:30 A Select Color dialog box opens.
08:33 Click on any color to select. Click on OK button.
08:38 Observe the panel, the colors of the orbitals are now changed. Close the dialog box.
08:45 To remove the orbitals from the structure;Un-check the Surfaces option in the Display Types.
08:51 Click on Vibrations tab to view the vibrational frequencies.
08:56 In the Vibration window, click on any frequency from the list.
09:01 Click on Start Animation button present at the bottom of the window.
09:06 Observe the panel. The stretching of C-C and C-H bonds are animated.
09:13 We can also view the IR spectrum for the structure.
09:17 Click on Show Spectra.
09:20 A Spectra Visualization window opens. It shows the calculated IR spectrum of Benzene.
09:27 Open a new window. Open the log file created for water molecule using GAMESS programme.
09:35 The log file opens with a structure of water and Molecular orbital information.
09:41 Click on the name of the orbital from the list. The orbital is displayed on the panel.
09:47 Let's summarize
09:49 In this tutorial we have learnt to, Prepare the input files for computational chemistry programmes such as: GAMESS and Gaussian.
09:58 View Molecular orbitals for benzene and water molecules.
10:04 View calculated IR spectrum for molecules using log files generated from Gaussian.
10:11 For Assignment, Open the log file for benzene molecule from the code files provided.
10:18 Display any Molecular Orbital from the list.
10:22 Change the display and color of the lobes. Save the image in JPEG format.
10:29 This video summarizes the Spoken Tutorial project If you do not have good bandwidth, you can download and watch it.
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10:42 The Spoken Tutorial Project is funded by NMEICT, MHRD Government of India.
10:48 This is Snehalatha from IIT Bombay signing off.

Thank you for joining.

Contributors and Content Editors

Jyotisolanki, PoojaMoolya