Fig. 5: Molecular dynamics simulation.
From: Gamma estimator of Jarzynski equality for recovering binding energies from noisy dynamic data sets
a The calculated potential of mean force (PMF) using adaptive biasing force method. After 400 ns simulation, the solution converges. b Snapshot of peptide conformation in the window centered at 1.5 nm; when the distance of the mass center of all the alpha carbons of the peptide from surface is ~1.2 nm, the N-terminal touches the surface and stays for a while, which corresponds to the plateau around 1 nm shown in (a). c Snapshot of peptide conformation in the window centered at 0.9 nm. d Snapshot of peptide conformation in the window centered at 0.3 nm. The center-of-mass is represented by a red sphere.
