This is an old revision of the document!
(The files for the programs mentions below can be found here hydrate_java_programs.zip )
Program: Minimize Dipole
Function:
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.
Steps:
1) Get coordinates of oxygen atoms in the from of pdb file (make sure entire file only contains oxygen atoms)
- Coordinates for hydrate crystal can be found on www.crystallography.net
2) Provide absolute path of this file in “Driver.java” on line 20
3) Provide absolute path of where you would like the output pdb file to be stored in “Driver.java” on line 21
4) Provide the coordinates of the center of the hydrate structure in “Driver.java” on line 14
- For example, if the hydrate begins at the origin, the center is just the dimensions of the cell divided by 2
5) Check “Driver.java” lines 8-10 to make sure the values correspond to the desired model of water
6) After you have modified the things above, compile the java code and run it to output the desired pdb file
Program: Fill Cages
Function:
This program generates the coordinates for the molecules that fill the cages of the hydrates.
Steps: (in “Driver.java”)
1) Input the right number for hydrate structure (1 or 2) on line 8
2) Uncomment the appropriate line for the structure number you have inputed on lines 12-13
- 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 in pdb format the coordinates of the molecules that fill the cages of the hydrate structure you have specified.
5) copy this output and append it to the pdb file for the hydrate crystal generated via Minimize Dipole
If you have any question, feel free to email me at kmanayer(at)yahoo(dot)com