Disordered Crystals


Well, well, well, what have we here? A crystal with disorder??? It can be indeed. Some times molecules jump between orientations, in this way they can "follow" the symmetry of the crystal cell. The result is that you might have a "fractional occupancy", meaning, in a site you might have 25% of the times a Chlorine atom, and 75% of the times a Carbon atom. So how do we deal with that?? Well, I have done some coding to do that. Let's start by the beginning:

  • First of all you must generate one single unit cell with mercury (as described here). The result will be molecules with ALL possible groups in ALL possible positions.
  • Special care must be taken to have the minimum number of molecules in the unit cell able to reproduce the whole crystal. If you don't do that, when you replicate the cell, mlecules will superpose at the edges of your simulation box giving as a result infinite forces, and the disgusting "segmentation fault" message (i.e. your system exploted!)
  • Now is the time to replicate the unit cell using the genconf command
      • gmx genconf -f crystal_one.pdb -o crystal_box.gro -nbox 5 5 5
  • Please do have into account what I explained here about spanish omelette. Do not equally replicate the unit cell if the lattice is skewed!
  • Now is time to randomize the structure by choosing only some of the groups your CIF has generated. You do that with the "control" program of ANGULA. The option to be used is rndstructure.
  • Finally you will probably wish to change the atomic ordering or names using the CONTROL option: edit_pdb
Hope this helps