building_a_hydrate_lattice
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| - | **(The files for the programs mentions below can be found here {{hydrate_java_programs.zip}} )** | + | **(The files for the programs mentions below can be found here {{Avicci.zip}} )** |
| - | __**Program: Minimize Dipole**__ \\ | + | **__Overview__** |
| - | __Function: | + | To build the gas hydrate lattice, you need to obtain the coordinates of the oxygen atoms in a unit cell and use the program Avicci to insert hydrogen atoms in such a way as to minimize the overall dipole of the unit cell while abiding by the Bernal–Fowler ice rules. The program then fills the cages of hydrate slab as the the input specifies. |
| - | This program takes in the coordinates of oxygen atoms of a structure I and structure II hydrates and adds the hydrogen atoms to form water molecules. The hydrogen atoms are added in accordance with the ice rules while minimizing the local and global dipole moments of the hydrate. The results are outputted in the form of a pdb file. The program can generate water molecules to work with TIP4P-EW and TIP4P-2005 models of water. | + | **__Getting Oxygen Atom Coordinates__** |
| + | 1- Go to http:// | ||
| + | 2- Click on Search under Accessing COD Data on the left side \\ | ||
| + | 3- Search by DOI: 10.1021/ | ||
| + | Paper associated with above DOI: | ||
| + | "Gas Hydrate Single-Crystal Structure Analyses by | ||
| + | Michael T. Kirchner, Roland Boese, W. Edward Billups, and Lewis R. Norman | ||
| - | __Steps:__ \\ | + | - For structure I, use COD ID: 4112809 |
| + | - For structure II, use COD ID: 4112807 | ||
| - | 1) Get coordinates of oxygen atoms in the from of pdb file (make sure entire file only contains oxygen atoms) \\ | + | 4- Click on " |
| - | * Coordinates for hydrate crystal can be found on www.crystallography.net | + | |
| - | 2) Provide absolute path of this file in " | + | |
| - | 3) Provide absolute path of where you would like the output pdb file to be stored in " | + | - You can use the software Avagadro |
| + | - You can download Avagadro from here: https:// | ||
| - | 4) Provide | + | 5- Open the .cif file with Avagadro |
| + | 6- You will see a unit cell for the structure \\ | ||
| + | 7- Click on Build-> | ||
| + | 8- Sort by Element \\ | ||
| + | 9- Delete all the non-oxygen atoms and their coordinates | ||
| + | - (delete all lines that do not start with the letter O) \\ | ||
| + | 10- Click apply and exit out of the Cartesian Editor \\ | ||
| + | - You should see a less crowded unit cell with only the Oxygen atoms \\ | ||
| + | - Now we will save the coordinates as a .pdb file \\ | ||
| + | 11- Click on " | ||
| + | (see 4112809_justOxygen.cif and 4112807_justOxygen.cif) | ||
| - | * For example, if the hydrate begins at the origin, the center is just the dimensions of the cell divided by 2 \\ | ||
| - | 5) Check " | ||
| - | 6) After you have modified the things above, compile the java code and run it to output the desired pdb file | + | **__Using Avicci__** |
| + | You will need to have Java installed to use this program. | ||
| + | Click on Avicci.jar to launch the program \\ | ||
| - | __**Program: Fill Cages**__ \\ | + | __Specify the inputs:__ \\ |
| - | __Function:__ | + | - __Input path:__ Enter the absolute path for the .pdb file that contains the coordinates of the oxygen atoms \\ |
| - | This program generates | + | - __Output path:__ Enter the absolute path for the .pdb file that will contain |
| - | __Steps:__ (in " | + | - __Structure:__ Enter 1 for structure I or 2 for structure II \\ |
| - | 1) Input the right number for hydrate | + | - __Fraction Methane in Small Cages:__ Enter a value between 0 and 1 inclusive (All cages in structure |
| - | 2) uncomment the appropriate line for the structure | + | - __Fraction Methane in Large Cages:__ Enter a value between 0 and 1 inclusive (input ignored |
| - | * this number is the length of one side of the cubic hydrate cell \\ | + | |
| - | 3) Input the right values on lines 21-24 | + | |
| - | * Unordered List ItemTSM => fraction of small cages that should be filled with Methane | + | |
| - | * In structure 1 hydrates, all cages are considered small cages | + | |
| - | * TLC => fraction of large cages that should be filled with Cyclohexane | + | |
| - | * TLB => fraction of large cages that should be filled with Benzene | + | |
| - | * Unordered List ItemTLM => fraction of large cages that should be filled with Methane | + | |
| - | 4) Comple the java code and run it to output via the console | + | - __Fraction Cyclohexane |
| - | 5) copy this output | + | - __Fraction Benzene in Large Cages:__ Enter a value between 0 and 1 inclusive (input ignored |
| + | - __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.1524185759.txt.gz · Last modified: 2018/04/19 20:55 by edit