Builder (packmol)

To build systems consisting of many different molecules, randomly put together, the GUI includes the Builder. This is a graphical interface to the packmol program, using only a few possibilities of it. The most common use will be to set up a big system for Molecular Dynamics with Force Field, ReaxFF, ML Potential, or DFTB.

See also

The five starting modes of the Builder

The Builder can be started in five modes, depending on the current system when the Builder is launched:

  1. Packing in an empty box: The Builder is started for an empty system. The Builder will then pack the molecules and modify the lattice vectors of the system.

  2. Packing in an empty box, replacing current system: The Builder is started for a non-empty non-periodic system. This is identical to the previous mode. The current molecule is discarded. To pack the current molecule, first export it to a .in or .xyz file, and import the file from the Builder.

  3. Packing inside the crystal: The Builder is started for a non-empty 3D-periodic system. The Builder will then pack molecules around the existing system, into a space defined by the lattice vectors. The lattice vectors will not change.

  4. Packing around the slab: The Builder is started for a non-empty 2D-periodic system. This is similar to the previous mode, but you must specify the box bound along z.

  5. Packing around the chain: The Builder is started for a non-empty 1D-periodic system. This is similar to the previous mode, but you must specify the box bounds along y and z.

Tip

Activate the engine that you want to use for your calculation before starting the Builder, for example by switching from ADFPanel → ForceFieldPanel.

Why? The Builder is most commonly used to build a 3D-periodic system. However, the ADF engine (default in AMSinput) cannot handle 3D-periodic systems. If the ADF engine is active when you start the builder, then the lattice vectors will be removed when you close the builder, since ADF cannot handle them.

Note on non-orthorhombic systems

The Builder for periodic systems is most reliable if the lattice vectors are oriented along x, y, and z with 90 degree angles.

For non-orthorhombic systems, the Builder removes molecules that fall outside the unit cell. This usually means that you pack fewer molecules than you specify.

For non-orthorhombic systems, always carefully check the resulting structure to see if it matches your expectations.

The Builder has flexible input

The Builder has flexible input. This means that you specify only some of the input options, and appropriate or approximate values for the remaining input options will be automatically determined.

  • Density: The mass density of the molecules to be packed.

  • Approximate number of atoms: The approximate number of atoms to pack. Cannot be combined with Number of molecules (see below).

  • Box Dimensions (X, Y, Z): Pack the molecules into a box defined by these dimensions

  • Tolerance: Approximate interatomic distance between molecules. To allow for more tight packing, decrease this number.

  • Use number of molecules: Explicitly specify the number of molecules to pack in the N mols column.

  • Use mole fractions: Specify relative mole fractions of different components in the Mole fraction column. The actual number of molecules to pack is determined by other input options.

You can choose how many types of molecules to pack. Click the AddButton to add more molecules. For each type of molecule, you may specify:

  • SMILES or file: (i) SMILES code for a molecule: enter CCO for ethanol, or (ii) a file from the SCM library: enter ethanol and click on the match in the drop-down, or any file on disk: click the DirButton icon

  • N mols: The number of molecules to pack for this type

  • Mole fraction: Relative mole fraction for this molecule

  • Region: Assign a region name for this molecule. By default, all packed molecules are placed into a region called Builder.

Finally, there is an option to perform a Dry run. This will generate a Python script that you can use a starting point for running the Builder from Python (for example, to automate the generation of different box sizes, mole fractions, …).