When your two electrodes are of different materials, they may have a different work functions, i..e their fermi levels are different. When you form the two probe, at zero bias the two fermi levels are alligned and it is now the two vacuum levels that are different. In the output file we report the value of the fermi levels, lets call that value Ef
Now you put in a metallic region as gate. If you specify the gate potential to zero, it will correspond to modelling a gate material with work function W=-Ef with a applied gate potential zero. However, if you would like to model another gate material with work function W1, you actually need to apply a potential V to simulate the situation of a zero gate potential V1=0.
Thus, the relation between the experimental gate potential V1, and the calculational gate potential V, is
V = V1+W1+Ef
Thus, if you have a calculation with Isd versus Vgate, you can transform it to a physical gate using the transformation
V1 = Vgate - (W1+Ef)