The present invention provides an evaluating system and the use thereof for the efficacy of antimicrobial peptide, which includes the following steps: (a) constructing a peptide by a first input unit, and load the peptide into an aqueous solution for a first time for equilibration; (b) constructing a lipid bilayer by a second input unit, and load the lipid bilayer into an aqueous solution for a second time for equilibration; (c) Using a first processing unit, simulations are carried out for an aqueous system containing an equilibrated peptide from the first input unit and the equilibrated lipid bilayer from the second input unit; (d) calculating the partition free energy of the peptide by a second processing unit; (e) outputting the prediction by an output unit, wherein the output unit is connected with the first processing unit and the second processing unit. |