Navigating in foldonia: Using accelerated molecular dynamics to explore stability, unfolding and self-healing of the β-solenoid structure formed by a silk-like polypeptide
Fig 11
Illustration of aMD simulation.
Graph of V(r) versus r showing a low threshold potential energy, E, (black horizontal line) and a high threshold potential energy, E’, (blue horizontal line). In an aMD simulation, a boost ΔV(r) is added to the original potential energy landscape V(r) when the system potential or the dihedral energy is lower than the predefined threshold E, resulting in the boosted potential energy, V*(r) (dashed red line). Regions of the potential energy curve that are above the threshold energy maintain their original form. If the threshold energy is increased to E’, a larger boost potential energy, ΔV’(r) is added to the original free energy. In that case another free energy minimum goes below the new threshold, E’, resulting in a boost potential added to that region. The shape of the energy surface and the position of the energy minimum remain the same after adding the boost.