Packmol

Download Packmol from http://www.ime.unicamp.br/~martinez/packmol/ and follow the installation instructions.

Create an input file named input.inp. Here is an example:

                  tolerance 2.0 # tolerance distance
                
                  output ionic2.pdb # output file name
                
                  filetype pdb # output file type
                
                  #
                
                  # Create a box of [bmim][BF4] and acetonitrile molecules
                
                  #
                
                  structure bf4.pdb
                
                  number 102 # Number of molecules
                
                  inside cube 0. 0. 0. 35. # x, y, z coordinates of box, and length of box in Angstroms
                
                  end structure
                
                  # bmim
                
                  structure bmi.pdb
                
                  number 102
                
                  inside cube 0. 0. 0. 35.
                
                  end structure
                
                  # acetonitrile
                
                  structure acn.pdb
                
                  number 154
                
                  inside cube 0. 0. 0. 35.
                
                  end structure

Run Packmol

                  $ packmol < input.inp
                

View the pdb file generated by packmol in Visual Molecular Dynamics (VMD):

Figure 8:

Structure arising from packmol

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