Decomposition of of GNNQQNY bilayers.

The most stable pattern (BBA1) is marked in bold, which also corresponds to the x-ray structure. The energy unit is kcal/(mol peptide) and temperature (T) is 300 K. is the sum of the four terms on its left (Eq. 1). Translational and rotational free energies for a monomer were kcal/mol and kcal/mol, which were subtracted from when calculating . Numbers in parentheses are obtained from simulations with 20 peptides. Due to size limitations of the NMA facility in CHARMM, was not calculated in the 20-peptide case under PBC, but it is expected to have only a minor contribution. Although energy terms individually vary between simulations with 12 and 20 peptides, in BBA1 is consistently lower than that of FFA1 by 2.92 kcal/mol (12 peptides) and by 2.35 kcal/mol (20 peptides).