building_a_hydrate_lattice
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building_a_hydrate_lattice [2018/05/08 11:34] – edit | building_a_hydrate_lattice [2018/05/08 11:48] (current) – edit | ||
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**__Getting Oxygen Atom Coordinates__** | **__Getting Oxygen Atom Coordinates__** | ||
- | 1- Go to http:// | + | 1- Go to http:// |
- | 2- Click on Search under Accessing COD Data on the left side | + | 2- Click on Search under Accessing COD Data on the left side \\ |
- | 3- Search by DOI: 10.1021/ | + | 3- Search by DOI: 10.1021/ |
Paper associated with above DOI: | Paper associated with above DOI: | ||
Line 15: | Line 15: | ||
Michael T. Kirchner, Roland Boese, W. Edward Billups, and Lewis R. Norman | Michael T. Kirchner, Roland Boese, W. Edward Billups, and Lewis R. Norman | ||
- | | + | - For structure I, use COD ID: 4112809 |
- | - For structure II, use COD ID: 4112807 | + | - For structure II, use COD ID: 4112807 |
- | 4- Click on " | + | 4- Click on " |
(see 4112809.cif and 4112807.cif) | (see 4112809.cif and 4112807.cif) | ||
- | You can use the software Avagadro to open the .cif file | + | |
- | You can download Avagadro from here: https:// | + | - You can download Avagadro from here: https:// |
- | 5- Open the .cif file with Avagadro | + | 5- Open the .cif file with Avagadro |
- | 6- You will see a unit cell for the structure | + | 6- You will see a unit cell for the structure |
- | 7- Click on Build-> | + | 7- Click on Build-> |
- | Sort by Element | + | 8- Sort by Element |
- | Delete all the non-oxygen atoms and their coordinates | + | 9- Delete all the non-oxygen atoms and their coordinates |
- | (delete all lines that do not start with the letter O) | + | - (delete all lines that do not start with the letter O) \\ |
- | click apply and exit out of the Cartesian Editor | + | 10- Click apply and exit out of the Cartesian Editor |
- | You should see a less crowded unit cell with only the Oxygen atoms | + | - You should see a less crowded unit cell with only the Oxygen atoms \\ |
- | Now we will save the coordinates as a .pdb file | + | - Now we will save the coordinates as a .pdb file \\ |
- | click on " | + | 11- Click on " |
- | (see 4112809_justOxygen.cif and 4112807_justOxygen.cif) | + | (see 4112809_justOxygen.cif and 4112807_justOxygen.cif) |
- | Using Avicci | + | **__Using Avicci__** |
- | You will need to have Java installed to use this program. | + | You will need to have Java installed to use this program. |
- | Click on Avicci.jar to launch the program | + | Click on Avicci.jar to launch the program |
- | Specify the inputs: | + | |
- | - Input path: Enter the absolute path for the .pdb file that contains the coordinates of the oxygen atoms | + | |
- | - Output path: Enter the absolute path for the .pdb file that will contain the final slab (include the name of the output file in the path) | + | |
- | - Structure: Enter 1 for structure I or 2 for structure II | + | |
- | - Fraction Methane in Small Cages: Enter a value between 0 and 1 inclusive (All cages in structure I are considered small cages) | + | |
- | - Fraction Methane in Large Cages: Enter a value between 0 and 1 inclusive (input ignored for structure I) | + | |
- | - Fraction Cyclohexane in Large Cages: Enter a value between 0 and 1 inclusive (input ignored for structure I) | + | |
- | - Fraction Benzene in Large Cages: Enter a value between 0 and 1 inclusive (input ignored for structure I) | + | |
- | - Water Model ( 1 for TIP4P-EW , 2 for TIP4P-2005 ): Enter 1 or 2 | + | |
- | - Slab Size A: Size of final slab in the X direction as a multiple of the unit cell size, Enter a value greater than zero | + | |
- | - Slab Size B: Size of final slab in the Y direction as a multiple of the unit cell size, Enter a value greater than zero | + | |
- | - Slab Size C: Size of final slab in the Z direction as a multiple of the unit cell size, Enter a value greater than zero | + | |
- | Example: A = 2 , B = 2 , C = 1 creates a 2 X 2 X 1 slab of the unit cell in the input file | + | |
- | - Number of spaces to 1st coordinate: Number of words/ | + | |
- | Click " | + | __Specify |
+ | - __Input path:__ Enter the absolute path for the .pdb file that contains the coordinates of the oxygen atoms \\ | ||
- | (see 4112809_justOxygen_output.cif and 4112807_justOxygen_output.cif) | + | - __Output path:__ Enter the absolute path for the .pdb file that will contain the final slab (include the name of the output file in the path) \\ |
+ | - __Structure: | ||
+ | |||
+ | - __Fraction Methane in Small Cages:__ Enter a value between 0 and 1 inclusive (All cages in structure I are considered small cages) | ||
+ | |||
+ | - __Fraction Methane in Large Cages:__ Enter a value between 0 and 1 inclusive (input ignored for structure I) \\ | ||
+ | |||
+ | - __Fraction Cyclohexane in Large Cages:__ Enter a value between 0 and 1 inclusive (input ignored for structure I) \\ | ||
+ | |||
+ | - __Fraction Benzene in Large Cages:__ Enter a value between 0 and 1 inclusive (input ignored for structure I) \\ | ||
+ | |||
+ | - __Water Model ( 1 for TIP4P-EW , 2 for TIP4P-2005 ):__ Enter 1 or 2 \\ | ||
+ | |||
+ | - __Slab Size A:__ Size of final slab in the X direction as a multiple of the unit cell size, Enter a value greater than zero \\ | ||
+ | |||
+ | - __Slab Size B:__ Size of final slab in the Y direction as a multiple of the unit cell size, Enter a value greater than zero \\ | ||
+ | |||
+ | - __Slab Size C:__ Size of final slab in the Z direction as a multiple of the unit cell size, Enter a value greater than zero \\ | ||
+ | |||
+ | Example: A = 2 , B = 2 , C = 1 creates a 2x2x1 slab of the unit cell in the input file \\ | ||
+ | |||
+ | - __Number of spaces to 1st coordinate: | ||
+ | |||
+ | Click " | ||
+ | \\ | ||
+ | \\ | ||
+ | |||
+ | If you have any question, feel free to email me at kmanayer(at)yahoo(dot)com | ||
building_a_hydrate_lattice.1525793673.txt.gz · Last modified: 2018/05/08 11:34 by edit