5.12 Build a solvent cluster OpenGL

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

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

 

5.12.1 The graphic interface

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

 
Cluster builder     Single acetone molecule

Ordered acetone cluster

Clicking the Auto button, the cell size is assigned automatically by the monomer dimensions considering the covalent radii of each atoms. Clicking the Build button, the cluster is generated. With the parameters showed in the above dialog box, VEGA creates an ordered cluster.
If you want 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 for all three axis).

    Chloroform monomer

Chloroform cluster

Chloroform cluster (zoomed)

If the cell size is too small, the bump possibility 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. The user can specify the 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 showed 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.