How to build up a supercell for explicit solvent system?

Question

I would like to construct the supercell that contains explicit 4 ionic liquid molecules (i.e. $[EMIM][BF_{4}]$) for running AIMD. Is there any recommended software or code that is suitable and easy to generate the structure? I am not sure that Atomic Simulation Environment can help since it usually focuses on the solid structure.

Answer 1

1. Using ASE GUI

You can utilize ase gui to build supercell manually. Open ASE GUI window with two molecules (for example ase gui emim.xyz bf4.xyz). Then create new window and create a unit cell, copy & paste the molecules, rotate & move to fit the cell.

2. Using packmol

packmol is actually more common tool for this kind of task. It randomly packs molecules in simulation box.

For AIMD simulation you should be careful because packmol does not support PBC. So if the desired size of supercell is 15 x 15 x 15, it is recommended to pack molecules in slightly smaller box and set periodic unit cell later.

For example, the input file pack.inp looks like:

filetype xyz

tolerance 2.0  # intermolecular distance limit

output supercell.xyz


# 4 emim and 4 bf4 inside 13 x 13 x 13 box

structure emim.xyz
  number 4 
  inside box 0. 0. 0. 13. 13. 13.
end structure

structure bf4.xyz
  number 4
  inside box 0. 0. 0. 13. 13. 13.
end structure

Now you can impose PBC using ASE:

import ase.io
import ase.build

atoms = ase.io.read("supercell.xyz")
atoms.cell = [15, 15, 15]
atoms.pbc = [True, True, True]
atoms.center() # Just for easy visualization
# If you use VASP:
atoms = ase.build.sort(atoms) 
atoms.write("POSCAR")
```

Answer 2

You might find the Avogadro software (old v1.20) useful for this work. You can create a specified cell (Crystallography>>Add unit cell) and copy and paste the structures you might already have (in xyz format), or create those in another window of Avogadro, pre-relax it using the classical fields available in Avogadro and copy-paste it inside the cell.

Be careful of periodic boundaries as the molecules might be very close to each other in the images.