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. Author manuscript; available in PMC: 2020 Aug 7.
Published in final edited form as: Cell Rep Phys Sci. 2020 Jul 1;1(7):100085. doi: 10.1016/j.xcrp.2020.100085

Figure 6. All-Atom Molecular Dynamics Simulations.

Figure 6.

(A) Initial structure and a snapshot after 50 ns of MD simulation of the 1-KMe3 filament with fion = 0.5; fion specifies the number of ions per layer of peptide orthogonal to the filament axis. Water and ions are omitted for clarity, and black bars represent periodic boundary of the simulation box.

(B) Elongated length of the filament after 120 ns of MD simulation for different systems (1-KMe3 and 1P-KMe3 with different number of placed ions in the filament core). Error bars represent standard deviation.

(C) Distribution of water (red) and cations (yellow) within the filament (gray) in the initial structure and a snapshot after 50 ns of MD simulation of the 1-KMe3 filament with fion = 0.5.

(D) The number of water molecules that are maintained within the filament at the end of 120 ns of MD simulation for different systems. Error bars represent standard deviation.

The error bars in (B) and (D) are obtained using the last 10 nanoseconds of three independent 120 ns MD simulations.