Summary of simulated configurations.

Orie.: Orientation, P/A: Parallel/Anti-parallel ��-sheets. The protonation status of titratable groups at termini and charged side chains was determined based on pH in the experimental condition. The inter peptide distance (d) was either fixed or adjusted (adj.) using a constant pressure method. FBC: Free (not periodic) boundary condition. Numbers in parentheses after d are lengths of explicit-water production runs in nanoseconds. For some peptides, simulation times vary among different patterns, thus are given as ranges. Although the selection for the most stable bilayer patterns became clear usually within the first 2 ns of the production run (except for KLVFFAE at pH 7.0), a more converged profile of required longer simulation time, as explained in the text, and in Figs. 1, S1, and S4�CS8. Thus we extended simulation time for selected (NNQQ, VEALYL,and STVIIE) or all (GNNQQNY and KLVFFAE) bilayer patterns. : the number of peptides in a single ��-sheet. Considering multiple bilayer patterns tested for each peptide, the total length of production runs in explicit water was over 290 ns.