The initial conditions editor is where the user can add, edit and remove initial conditions. Initial conditions are the complexes that are present at the beginning of a simulation. Each initial condition represents one or more complexes that are present at the same abundance (defined as the number of molecules per reaction volume). Generally, each complex is defined as its own initial condition, even if multiple complexes have the same initial abundance.

The existing initial conditions are listed, along with their abundances, on the left hand side of the editor. The user can select an initial condition from the list to edit it in the right side of the editor. The selected initial condition can also be deleted via the Delete button in the top left of the editor. Click on the "New Species" button in the top left to create a new initial condition. On the right side of the editor, the user can add agents, states and bonds to the diagram. No site may be omitted on an agent in the initial conditions because the initial makeup of the system must be fully described. For the same reason, all bonds must be connected at both ends (no "any" and "wild-card" bonds are allowed). See Complex Editing for more details on how to draw complexes in Cellucidate. At the bottom right of the editor you can enter or edit the Kappa string for the initial condition. Next to the Kappa string is a text box where the user can enter the quantity (abundance) for the current initial condition.

After making changes to the initial conditions, hit the "Save Changes" button in the bottom right. To exit without saving any changes to initial conditions, click the "Cancel" button in the bottom right, or the (x) in the top right of the editor.