6.15 Build a solvent cluster

By this dialog box, that can be shown selecting  Edit Build Cluster menu item, it 's possible to build a solvent cluster useful for the solute solvation (for more information, click here). In order to create a new solvent cluster usable by VEGA ZZ, you should follow these steps:

  1. Generate the cluster with this tool.
  2. Optimize it by MM/MD software (e.g. NAMD, Gromacs, etc).
  3. Convert the optimized structure in PDB Fat format enabling bzip2 compression.
  4. Rename the file, removing the file extension and capitalizing the name.
  5. Copy the file to Data\Cluster directory.

 

6.15.1 The graphic interface

The following dialog box allows to build a cubic solvent cluster, specifying the dimensions of the box containing a single solvent  molecule (Cell size) and the number of cell copies in X, Y, and Z directions (Cell copies).

 

Cluster builder   Arrow  Single acetone molecule

Ordered acetone cluster

Clicking Auto, the cell size is assigned automatically by the monomer dimensions, considering the covalent radii of each atom. Clicking Build, the cluster is generated. The parameters shown above allow to create an ordered cluster.
If you want to obtain a disordered system, you must check Enable in Random rot. group-box, specifying the X, Y and Z  ranges used to generate the random rotation of each monomer placed in the cluster.

 

Rantom rotation enabled

This is an application example: a chloroform cluster is built using random rotation with 360º rotation ranges (the same value for all three axis).

   Arrow  Chloroform monomer

Chloroform cluster

Chloroform cluster (zoomed)

If the cell size is too small, the bumping probability between close monomers is high. It's possible to reduce this problem, checking Minimize bumps in the Optimization group-box. The position and the rotation of each monomer placed in the cluster is minimized using the fast Hooke-Jeeves algorithm. You can indicate number of minimization Steps and the RMS. The Overlap field contains the value of the maximum atom overlapping between two near molecules. Enabling Remove molecules, the bumping molecules that can't be optimized, are automatically removed from the cluster.

Clicking View 3D cell, a transparent box is shown in order to highlight the cell dimension. The magenta cross indicates the molecule symmetry center. You can change the molecule orientation in the cell using the move molecule function that can be enabled selecting Move Molecule item in the popup menu.

 

Cell view