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Intsallation of GAMESS on OSX Lion

GAMESS will not run on CASE SENSITIVE OSX filesystems. This will most likely not apply to you, as few people use case sensitive. You can check this via Disk Utility. In addition, GAMESS will not function properly if the name of your hard drives or folders have spaces and/or numbers in their names. Verify you meet these requirements before you start!

After you download the GAMESS binary for your system, you will have a compressed file, similar to the one pictured.

Drag the file to your HOME folder. It is the folder in your Finder side bar that looks like a little house.

Alternatively, if your home folder does not appear in the side bar, you can go to the menu at the top of the screen (make sure the BOLD black word next to the black apple in the very top left corner of your screen says 'Finder') and select: Go > Go to folder... In the dialog box that pops up, type a tilde (~) and hit Go or Enter.

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Decompress the archive.

Right-click the gamess-OSX.Current.x86-64.tar.gz file. Choose: Open>Open With>Archive Utility. Optianlly, you can double-click the gamess-OSX.Current.x86-64.tar.gz file to decompress it.

Wait for the file to decompress.

A diolog box will pop up, wait for it to complete.

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Double click on the 'gamess' folder that appears after the file finishes unpacking, it's contents should look something like the picture below:

You're now halfway there!

Next we need to download Molecular Visualization Software, to generate input files for GAMESS.

The package we will be using is called Avogadro, and is available here: http://avogadro.openmolecules.net/wiki/Main_Page Avogadro is completely free and open-source. It runs on Mac, Windows and Linux, and is geared toward interfacing with computational chemistry packages.

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Navigate to your download folder.

Decompress the .zip file:

Double-click the .zip file. You will see a status window open just as when you decompressed GAMESS. Wait for it to complete.

Open the .dmg installer file. Locate the newly decompressed file, ending in .dmg

Double-click the .dmg file to mount the disk image.

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You will get another dialog box:

Wait for it to complete.

Another window will now open:

Just drag the Avogadro icon to the Applications folder alias right next to it. This will copy it to your application folder automatically. You are now ready to set up and run your first computational job! Lets calculate the vibrational frequencies of a water molecule.

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Open Avogadro in your Applications folder. You access this from your sidebar, as shown above.

The basic interface will look like this.

Pick the type of molecular view you'd like to use:

There are many options and different ways to view your molecular structures. Later, come back and play with the different styles, in order to find one you like best. The little wrenches next to some of the view types allow you to customize the view even further.
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For now, check the box next to 'Ball and Stick'

Insert a fragment from the built-in fragment library:

Go to the TOP menu, making sure the BOLD word says 'Avogadro', as pictured. Select: Build > Insert > Fragment...

From the fragment library choose water:

The pre-built fragments are extensive, and more can be added to the library easily. For now, find the water.cml fragment file, higlight it, and click insert fragment.
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There should now be a water molecule in the main viewer area.

Your mouse wheel can be used to zoom in or out. Try this now.

Use the navigation tool to view the molecule from different angles.

The navigation tool looks like a small, blue star in the upper left corner of your screen. Follw the instructions to manipulate your molecule until you are comfortable viewing it in 3D.

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Optimize the geometry of our molecule.

In order to save our CPU from as much work as possible, let's use molecular mechanics to quickly perform a pre-run optimization of molecular geometry. This will make our computational calculation go faster. In the top menu choose: Extensions > Optimize Geometry You will see the geometry of the molecule change, and the calculations performed in the message window just below the molecule viewer.

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Prepare the input file for our computational job:

The next step is to open the GAMESS input generator. This will let us choose from from various computational job types, and will 'translate' the picture of our molecule into an array of numeric coordinates that GAMESS can understand. In the TOP menu, choose: Extensions > GAMESS > Input Generator...

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The input Generator will look like the picture below:

The numbers I placed on top of the Input Generator window are: 1.) The type of calculation to be performed. 2.) The theory and basis set to be used to caculate the desired observables. 3.) The solvent, multiplicity, and charge for the calculation. 4.) The actual text output that GAMESS will recieve. This is update in real time as you make changes to the options.

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Set up your first job:

For now let's calculate the vibrational frequencies. The only box we need to change is the CALCULATE box. Click on it, and set it to FREQUENCIES.

Save the input file:

1.) Click the 'Generate...' button. 2.) Enter a name for your input file. 3.) Save the input file somewhere you'll remember. In this case I have it set to save into the
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GAMESS folder. You'll probably want to eventually make a special folder to hold your computational jobs. 4.) Hit Save

Now navigate to your GAMESS folder:

You should see your .inp file in the folder. Double-click the GamessQ icon.

A configuration window should open.

NOTE: If your configuration window does not open automatically, you can access it via the TOP menu:

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GamessQ > Preferences... or by holding command + , (command and the comma key)

Set up the Spool folder:

1.) Click the 'Browse...' button next to the Spool Directory window. 2.) In the dialog window that opens, choose: Home > gamess > spool Highlight the FOLDER only (in the above picture the gamess folder is highlighted, it should be the Spool folder) 3.) Click Choose Repeat this procedure for the GAMESS Path, but highlight the gamess folder instaed and click choose.

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Run the job

Click the add button, and choose your input file in the dialog box that pops up. Remember, it's in: Home > gamess and has a .inp extension.

Choose the number of cores for the job:

For now, leave this at one. Multi-core jobs are much more difficult to set up. Hit OK, and your job should start to run!

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Watch the GamessQ for your job to complete!

When you see the status of your job change to done, GAMESS has finished calculating our vibrational frequencies. Let's see the results!

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