Table 1 All-atom (AA) and coarse-graining (CG) simulation set-ups utilized in this work. For Decoralin, NK-1, and Temporin-L all set-ups were performed except CG simulations with POPC vesicles.
Forcefield | System | # Peptides | Pressure (bar) | Temperature (K) | Time (μs) | |
|---|---|---|---|---|---|---|
Bilayer Membrane (AA simulations) | Amberff99sb-ildn-NMR (peptides) SLipids (lipids) | POPC:POPG (1:1) 64 lipids per leaflet | 1 | 1 | 323 | 2 |
Vesicle (CG simulations) | Martini3 | POPC:POPG (1:1) (Outer: 1722 lipids) (Inner: 1106 lipids) | 28 | 303 | 10 | |
141 | 10 | |||||
283 | 50 | |||||
565 | 50 | |||||
848 | 50 | |||||
POPC (Outer: 1701 lipids) (Inner: 1057 lipids) | 28 | 10 | ||||
138 | 10 | |||||
276 | 10 | |||||
551 | 10 | |||||
827 | 10 |
