Klauda Lab Simulation Wiki

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**(The files for the programs mentions below can be found here {{Avicci.zip}} )**

**__Overview__**

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. 

**__Getting Oxygen Atom Coordinates__**

 1- Go to http://www.crystallography.net/cod/ \\
 2- Click on Search under Accessing COD Data on the left side  \\
 3- Search by DOI: 10.1021/ja049247c  \\

    Paper associated with above DOI: 
    "Gas Hydrate Single-Crystal Structure Analyses by
    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  \\

 4- Click on "CIF" under next to the COD ID to download the .cif file 
    (see 4112809.cif and 4112807.cif)

 - You can use the software Avagadro to open the .cif file  \\
 - You can download Avagadro from here: https://avogadro.en.softonic.com/  \\

 5- Open the .cif file with Avagadro  \\
 6- You will see a unit cell for the structure \\
 7- Click on Build->Cartesian Editor \\
 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 "File->Save as", select PDB under "Save as type" and save the file \\
    (see 4112809_justOxygen.cif and 4112807_justOxygen.cif)


**__Using Avicci__**

You will need to have Java installed to use this 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 2x2x1 slab of the unit cell in the input file \\

- __Number of spaces to 1st coordinate:__ Number of words/spaces before the x-coordinate in the input .pdb file, used for parsing the coordinates (Enter 5 as the default value)   \\

Click "Generate Hydrate" to execute the program and close the program. Check the ouptput path for the results of the program.  \\
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If you have any question, feel free to email me at kmanayer(at)yahoo(dot)com  \\