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.
You can select the type of solvent by
the combo-box, but it's also possible to specify an external cluster file
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.
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 (side = 20 Å)|
|Water sphere (radius = 10 Å)|
|Water layer (thickness = 4 Å)|