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. 2023 Sep 2;15(9):542. doi: 10.3390/toxins15090542

Table 1.

Summary of molecular dynamics simulations.

Simulation Systems Sampling Method The Initial Conformation Two Collective Variables (CVs) Acronym Simulation Length (ns)
Tetramer AapA1-28/POPE/POPG (3:1) CMD simulation Figure 1A CMD_T1 5000 ns
Figure 1B CMD_T2 5000 ns
AapA1-28/POPE/POPG (3:1) 2D-MetaD simulation Figure 3C CV1: Contact number between K-23 and the top phosphate group.
CV2: Contact number between K-23 and the bottom phosphate group.
WT1 2 replica× 1000 ns
AapA1-28/POPE/POPG (3:1) 2D-MetaD simulation Figure 3D The same CVs WT2 2 replica ×1000 ns
AapA1-28/POPE/POPG (3:1) CMD simulation Figure 5A (representative conformation of region A in Figure 4) CMD_M1 1000 ns
Figure 5B (representative conformation of region B in Figure 4) CMD_M2 1000 ns
Figure 5C (representative conformation of region A’ in Figure 4) CMD_M3 1000 ns
Figure 5D (representative conformation of region B’ in Figure 4) CMD_M4 1000 ns
Figure 5E (representative conformation of region C’ in Figure 4) CMD_M5 1000 ns