Finite system and periodicity effects in free energy simulations of membrane proteins

Periodic boundary conditions are routinely used in molecular dynamics simulations of biological systems, although they are inherently nonperiodic. Simulation artifacts that may arise from such artificial periodicity have not been well studied for membrane proteins. Here we investigate the finite size and periodicity effects in the gramicidin A peptide embedded in lipid bilayer, which offers a simple and well established test system. Comparison of free energies of translocating a potassium ion from bulk to the gramicidin A center in systems with different sizes indicate that there is no discernible effect on the free energy calculations due to finite system size and periodicity.