How to convert packmol output to VASP format?

Question

I want to model some cells with liquid water using VASP. I use the Packmol package to generate the initial configuration, but when I try to convert the pdb output file into the POSCAR format, the positions are completely messed up. This is the input file for Packmol, which places 17 H2O molecules in a 5x5x20 Angström box:

#
# A box with water
#

tolerance 2.0
filetype pdb
output water_box.pdb

structure water.pdb
  number 17
  inside box 0. 0. 0. 5. 5. 20.
end structure

This looks fine when I open the output file in VESTA, all molecules are within the stated confines with reasonable minimal distance:

But this structure contains no cell information. When I export the data as POSCAR format, the cell looks like this:

The positions are messed up and the minimal distance between molecules is not preserved. As such, some of these molecules are not recognizable as H2O anymore.

I get exactly the same result, when I copy the atomic positions from the .pdb file and place them in a POSCAR file manually.

How can I convert the pdb file into the POSCAR format properly?

Answer 1

I found a solution in the newest version of packmol, 20.15, which introduces orthorhombic periodic boundary conditions as feature. Before, I used 20.14, which lacks this feature.

I added a line with pbc 5.0 5.0 20.0, to enforce a 5x5x20 Angström box, so now my input file looks like this:

#
# A box with water
#

tolerance 2.0
filetype pdb
output water_box.pdb
pbc 5.0 5.0 20.0 

structure water.pdb
  number 17
  inside box 0. 0. 0. 5. 5. 20.
end structure

The output file now contains an additional line 6 headed with CRYST1, which contains the crystal box dimensions:

HEADER 
TITLE     Built with Packmol                                             
REMARK   Packmol generated pdb file 
REMARK   Home-Page: http://m3g.iqm.unicamp.br/packmol
REMARK
CRYST1     5.00     5.00    20.00  90.00  90.00  90.00 P 1           1
HETATM    1  H   HOH A   1       0.755   2.026   0.737                          
HETATM    2  H   HOH A   1       2.331   2.446   0.829                          
HETATM    3  O   HOH A   1       1.400   2.790   0.706
...   

VESTA now loads this file correctly. While it looks simple to add, I would caution against just adding this line in a file generated by earlier versions, since the periodic images are likely not considered there.