I would like to calculate commission which I pay to a different supplier

Firstly set up a commission type rate code 

Now set up the supplier record- setting the supplier type as Agency commission:

Now on the Assignment - On cost and commission tab set up the commission rules

Select the On cost & commission rate code as your rate code. 

Set the On cost & commission type as Direct to Supplier.

Set the On cost & commission paid to as the new supplier record.

Now add the commission rate rule:

The first rate code must be Gross Across Timesheet

When validating the timesheet you will see the commission line under the pay element of the timesheet.

Once the timesheet has been validated, this commission component will appear under Create purchase invoices:

Set the Payment Type as Commission Purchase invoice reconciliation, and then select your commission supplier: