6.10 Add a solvent cluster

Choosing Edit Add Cluster in the main menu, you can solvate a molecule with any type of solvent. The list of solvent is dynamically created, reading the ...\VEGA ZZ\Data\Clusters directory and can be refreshed closing and reopening the dialog window. Click here for more information about  the cluster file format.


Cluster calculation


You can select the type of solvent by the combo-box, but it's also possible to specify an external cluster file clicking the Open button.  The shape type (Box, Sphere and Layer) influences the meaning of Sides fields. If Type is Box, you can put the solvent box dimensions in Ångström. If Same is checked, the box will be cubic. If Type is Sphere, you can put the Radius of the cluster sphere in Ångström. If Type is Layer, you can specify the thickness of the solvent in Ångström. Overlap parameter indicates the maximum overlapping of the solvent-solute Van der Waals spheres. In Cluster position you can choose where the cluster is placed at the center of the box including the solute (Box center) or at the barycentre of the solute (Geometry center ). When you select Custom, you can specify the coordinates of the cluster centre. This feature is useful when you have to solvate with an asymmetric cluster (e.g. phospholipidic bilayer) and you want to place the solute in the middle. Checking Show the shape, a preview of the solvent shape is shown making easier the cluster setup. Clicking Calculate button, the cluster dimensions are automatically calculated on the basis of the solute size. This function isn't available if the shape type is set to Layer.
Click Ok to calculate the cluster.

Water box    Water box (side = 20 Å)
Water sphere (radius = 10 Å) Water sphere
Water layer Water layer (thickness = 4 Å)