Recent advances in non-equilibrium techniques for free energy determination have enabled new and more ambitious free energy simulations of biological systems. After an introduction to free energy simulation techniques, I will present our simulated results for permeation of trace amines through phospholipid bilayers and for the enthalpy of antimicrobial peptide aggregation. The experimental techniques used by my collaborators (lipid permeability via fluorescence quenching and isothermal titration calorimetry) will then be quickly described in order to compare our simulated results against values obtained from biophysical experiments.