Solvent Molecules Builder¶
The Solvent Molecule Builder allows you to add a sphere of solvent molecules around your molecular system.
How to use the solvent molecules builder¶
Select the Solvent: choose from the list of available solvents.
Adjust the radius of the solvent sphere: use the slider to change the radius of the solvent sphere. The number of solvent molecules that will be added is displayed at the bottom of the panel.
Change the solute factor: use the slider to change the solute factor to control how close solvent molecules can get to the solute (your existing molecular system). A solvent molecule will only be added if its atoms are not too close to any atoms in your solute, based on a distance calculation that includes the sum of atomic radii multiplied by this factor. The number of solvent molecules that will be added is displayed at the bottom of the panel.
Generate Molecules: click the ‘Generate Molecules’ button to add the solvent molecules to your system.
Finalize: use Close to accept and close the builder, or Cancel to discard it.
The solvent molecules will be positioned around either the center of your current selection or the center of mass of the entire molecular system if there is no selection.
The geometry of the added solvent molecules is based on data from MD (molecular dynamics) calculations and is not be optimized for proper interactions with your specific molecule.
If you add Water, all added water molecules will be identical (good to use as fragments). If you add Chloroform or Methanol, the added molecules will not be identical.