Fig. 6

Default random simulation box start configuration without compartment definition (compare Fig. 7) of a chemical ensemble that comprises 800.000 (bulk) water particles (excluded from display), 40.000 water particles (to be located inside a vesicle, colored cyan), 2.200 (oriented outer-vesicle) DMPC molecules (with SPICES line notation: TriMeNP[START]-DMPN(MeAc-6Et)(MeAc-6Et[END]) [25]), 1.800 (oriented inner-vesicle) DMPC molecules (with SPICES line notation: TriMeNP[END]-DMPN(MeAc-6Et)(MeAc-6Et[START]) [25]) and 500 Kalata B1 cyclotides. All molecules—except the Kalata B1 cyclotides which are derived from PDB file 1NB1 [47]–are generated as randomly-oriented spatial SPICES 3D tubes at random positions in the box. The 500 Kalata B1 cyclotides are also randomly distributed throughout the box but their individual amino acid backbone particle positions are set according to their spatial 3D structure (with the side chain particles collapsed onto their neighboring backbone particles). In addition, each Kalata B1 cyclotide is overall shrunk into a virtual sphere (with a volume that corresponds to its particles’ DPD volume) from which all other particles are excluded–thus a Kalata B1 cyclotide start size is somewhat smaller than its actual size during simulation. DMPC particle colors: DMPN (red), Et (olive), MeAc (orange), TriMeNP (blue). Kalata B1 backbone particles are shown in beige (all amino acid side chain particles are excluded from display) with the backbone particles that correspond to the characteristic hydrophobic spot of these peptides displayed in yellow