Bacteriorhodopsin (BR) is a membrane protein which pumps protons through th
e plasma membrane. Transmembrane BR helical segments are subjected to simul
ation studies in order to investigate the effect of bilayer environment in
various simulation conditions. A bilayer potential is introduced to the sys
tem to mimic the lipid membrane. The structures from the simulations are co
mpared with the experimentally determined structures in terms of geometrica
l properties. Electrostatic contribution to the helix packing is also inves
tigated. The simulation results show that the packing geometry of the trans
membrane helices is highly affected by the bilayer potential. The results o
btained from the simulations may be used for further simulation studies and
analysis in investigating transmembrane helix packing.