|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:
|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.
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.|
|05:57|| 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.|
|09:49||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.|
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