Avogadro/C4/File-Extensions/English-timed

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.
10:35	We conduct workshops using Spoken Tutorials and give certificates. Please contact us.
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, Sandhya.np14