Analysis of single MD

Job name: GS all - APP, 25 ns, v=0.1 m/s, k=1

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Flareplot frames range 1-1 / 200

NGL control:

Frame: 0 / 200
0 = PDB, 1-200 = DCD


Heatmap of unfolding of substrate (chain E) during simulation.

Color denotes a probability of presence of a hydrogen bond in subsequent parts of the simulation.

H - α-Helix, G - 310-Helix, I - π-Helix, E - Strand, B - Bridge, C - Coil, T - Turn.

Job info

GS Mode: all
Peptide substrate: APP
Substrate length [aa]: 33
Total length [ns]: 25
Membrane thickness [Å]: 31.0
SMD chain and residues: E 33
SMD velocity [m/s]: 0.1
SMD k [kcal/mol/Å2]: 1.0
SMD (x y z) [Å]: (-3.76 -0.096 -8.898)

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