Place script

The place script is to create a random starting configuration.
You can find sample files (copy them to your own subdirectory) in ~jkua/reac/start3 for example.
Look at the README file.

How to place several copies of two different molecules into a box:

1. geo should contain the first molecule. (You can get it from fort.98 of any previous run using your molecule.) Make sure geo2 is empty.
2. Edit control for the cell parameters and the number of copies of the first molecule. Change the random seed.
3. Run exe. If it hangs, look at fort.8 to see what's going on. Change the random seed and try again. If it "hangs" (i.e. looks like nothing is happening after quite a while) around the same place several times, increase the box size (cell parameters) and try again.

Presuming that the first placement was successful:

4. Copy the fort.15 file to geo2
5. Edit geo so that it now contains your second molecule.
6. Edit control for the cell parameters and the number of copies of the first molecule.
7. Run exe just like in Step 3. You may need to play around with it.

If the second placement was successful:

8. Concatenate geo2 and fort.15 into a new file called fort.54. Leave the first header and remove the additional one that should be in the middle of the file (from geo2 probably).
9. Run d2x2 which generates fort.55 which you can view in Molden to see if everything looks okay. (Save this file somewhere for future reference.)
10. Run xtob. The xyz file is fort.55. Answer yes to input cell parameters. Enter the cell parameters, e.g. 12 12 12, the angles should be 90 90 90, and there's no need to sort.
11. This generates a file called fort.15 that you will use as the starting geo structure for your simulation.

You will first need to minimize this structure.
Then you'll have to compress the box to the correct (desired) density.
Then you can run the MD simulation(s).