ARCHIVED: Build a molecule and run a Gaussian job in SEAGrid
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Build a molecule
- To open the NanoCAD editor, from the main menu on the home screen, click .
- At the top of the "Nanocad" window, read the summary of Nanocad commands. The commands are:
- Rotate: Drag gray space
- Translate:
Shift
-drag gray space - Zoom:
Ctrl
-drag gray space - Move atom: Drag atom
- Add atom:
Shift
-click gray space - Delete atom:
Shift
-click atom - Add bond:
Shift
-drag atom to atom - Delete bond:
Ctrl
-drag atom to atom - Select atom:
Ctrl
-click atom - Add double bond:
Shift
-drag between bonded atoms - Select group:
Ctrl
-Alt
-click atom
- If there is an example water structure, to erase it, click at the bottom of the "Nanocad" window.
- To build a new structure, at the bottom of the "Nanocad" window, click . The "Import Structure" window will open. Move the "Nanocad" window slightly below the "Import Structure" window so that both are visible.
- In the "Import Structure" window, the current element (default element is
H
) is the atom that you can place in the "Nanocad" window.To change the current element, in the "Change current element to:" field, enter an element name; for this example, enter
C
for carbon. Click .Note:Atom names start with uppercase letters. To select barium, for example, enterBa
. - To add a carbon atom,
Shift
-click in the gray area of "Nanocad" window; a gray carbon atom will appear. - In an area close to (not on top of) your first carbon atom,
Shift
-click to place a second carbon atom. If the atom is too close, you can delete it byShift
-clicking the atom. - To build a bond between your two atoms, you will
Shift
-drag from one carbon atom to the other:- Position your cursor over one of the carbon atoms. Hold down
Shift
and drag your cursor to the second atom. During the operation, you will see a line appear between your atom and your cursor. The two atoms will temporarily change color to match the background, indicating an active operation. - When you move your cursor over the second carbon atom, release (in this order) the mouse button and
Shift
key. A bond will appear between the two atoms, and their color will change back to deep gray.
- Position your cursor over one of the carbon atoms. Hold down
- To change the current element to oxygen, in the "Import Structure" window, enter
O
. Click . - In the "Nanocad" window,
Shift
-click near a carbon atom. A red oxygen atom will appear. - To build a carbon-oxygen bond,
Shift
-drag from one carbon atom to the oxygen atom. Because the carbon-oxygen bond in acetaldehyde is a double bond, you need to repeat this process one more time.You will see a double bond between the carbon and oxygen atoms.
- You now have all the heavy atoms in acetaldehyde; the only missing atoms are hydrogen. To add hydrogen, at the bottom of the "Nanocad" window, click . NanoCAD will add the four missing hydrogen atoms to your unfinished acetaldehyde molecule.
- The last step for building the acetaldehyde molecule is minimizing the current structure. At the bottom of the "Nanocad" window, from the Note:Nanocad has many template molecules to choose from. In the "Import Structure" window, click, , or to view them.
drop-down menu, choose either the (conjugate gradients) method or the (steepest descent) method to minimize the current molecule.
The acetaldehyde molecule is complete. You are ready to create a Gaussian input file for this molecule.
Create your Gaussian input file
- At the bottom right in the "Nanocad" window, from the Export drop-down menu, choose . The "Nanocad" window will disappear, and the the "Gaussian 03 Input GUI" window will open.
- From the menu, choose , then , and then .
- In the "Select Wavefunction Type" window that opens, choose .
- From the menu, select , and then .
- In the "Add Polarization and/or Diffuse Functions" window that appears, choose .
- In the "6-31G" window, under "Diffuse Functions", choose (the first option, not ).
- From the menu, select , and then .
- From the menu, select , and then (for electronic population analysis).
- In the "Pop Options" window that appears, from the "Output File" column, choose (for regular).
- In the "Gaussian 03 Input GUI" window, from the menu, choose .
- In the "Additional Keywords" window that appears, select options in the following order:
- The last option (
- Op:
6
- Ov:
7
- N:
3
These settings help some post-processing programs.
) opens an "Options for IOp" window. Set the following values:
- Op:
- To close the "Options for IOp" window, click . In the "Additional Keywords" window, click to add all the keywords to the job.
- In the "Gaussian 03 Input GUI" window, set the following parameters:
- %nproc:
16
- %lproc:
1
- %mem (in MB):
300mb
- Job Name:
Acetaldehyde optimization
- Charge:
0
- Multiplicity:
1
- %nproc:
- Click . You will be directed to the "Create Experiment" window with the Gaussian input you created.
This is document amtp in the Knowledge Base.
Last modified on 2019-11-22 10:26:50.