6.10 Add a solvent cluster
Selecting Edit -> Add -> Cluster main menu item, you can solvate a molecule with any type of solvent. The list of solvent is dynamically created, reading the VEGA\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 from
the combo-box, but it's also possible to specify an external cluster file
clicking the
button. The shape type (Box, Sphere and Layer)
influences the meaning of the Side fields. If the Type is Box,
you can put the solvent box dimensions in Ångström. If Same is checked,
the box will be cubic. If the Type is Sphere, you con type the Radius
of the cluster sphere in Ångström. If the Type is Layer, you
can specify the thickness of the solvent in Ångström. The Overlap
parameter indicates the maximum overlapping of the solvent-solute Van der Waals
spheres. Changing the Cluster position from Geometry center to Custom
is possible to specify the cluster position by its center coordinates. This is
useful if you have an asymmetric solvent cluster (e.g. phospholipidic bilayer)
and you want center the solute in it. Checking Show the shape, a preview
of the solvent shape is shown making more easy the cluster setup. Clicking the
button, the cluster dimension is automatically calculated on the basis of the
solute dimensions. This function isn't available if the shape type is set to Layer.
Just click Ok to calculate
the cluster, or Cancel to close the dialog.
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Water box (side = 20 Å) | |
Water sphere (radius = 10 Å) | ![]() |
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Water layer (thickness = 4 Å) | |