TABLE 1.

The names, descriptions, and durations of the atomistic simulations in this study

Simulation Set	Configuration and Simulations	Duration
Trilayer_equil	Both trilayer models (with ceramide and with SM) equilibrated in experimental surface tension without the peptide present.	Both trilayers: 650 ns
Peptide_water	The 4F peptide simulated in water, while the restraints were gradually discarded.	100 ps + 20 ns + 1 µs/20 ns
Helix_trilayer	Two helical peptides interacting with the trilayers. Six simulations (one extended) with varying initial configurations for both SM and ceramide.	Both trilayers: 5 × (150/200 ns) + 600 ns
Unfolded_trilayer	One peptide interacting with the trilayers. The partially unfolded peptide structure was taken from the end of the Peptide_water simulation.	Both trilayers: 400 ns
Free_energy	A total of 21 umbrella windows for both trilayers. One peptide with the trilayer. Initial frames were extracted from the Unfolded_trilayer simulation.	Most windows 50 ns, some extended to 200 ns
Annealing	The end structures of the extended Helix_trilayer simulations for the trilayer with SM heated up and subsequently cooled down.	3 target temperatures, 100 ns each