A Coarse-Grained Molecular Dynamics Simulation Using NAMD Package to Reveal Aggregation Profile of Phospholipids Self-Assembly in Water

Figure 3

Various aggregate structures of phospholipid molecules during 160 ns simulation time. Bead of atoms in phospholipid molecules are represented by colored lines. Phospholipid head groups are green or blue lines, brown for phosphate, glycerol backbone pink and green hydrocarbon tail groups, and purple for the double bonds in the tail groups. Water molecules are presented by light blue beads.

(a) Clusters of 1500 molecules DLiPE at 𝑡 = 14.4 ns. Water molecules are not presented for clarity purpose only

(b) Cup-like structure of 1500 molecules DLPE at 𝑡 = 124.8 ns. Water molecules are not presented for clarity purpose only

(c) Tube-like structure of 1500 molecules DLPE at 𝑡 = 96.96 ns. Water molecules are not presented for clarity purpose only

(d) Liposome of 1500 molecules DOPE at 𝑡 = 21.6–45.6 ns. This picture clearly shows some water molecules inside the liposome

(e) Deformed Liposome of 1500 DLiPS molecules at 𝑡 > 101.6 ns. This picture clearly shows some water molecules that still reside in the deformed liposome

(f) Planar bilayer of 1500 molecules DLiPE at 𝑡 = 133.6 ns