I haven’t worked with bio-like structures in a long time, so hopefully someone could point me in the right direction. I have a long (7 nm), very flexible chain of organics, which seems to switch between a “denatured” linear shape and a blob depending on the salt concentration. Looking at individual local angles or at the surface-accessible surface area does not really yield a definitive quantitative difference.
What would be a good way to quantify this switching? Thanks!
SAS and radius of gyration would be good observables.
But I would think you would need very long simulations to see such transitions, if you would see them at all. There is a risk that the system will be stuck in one of the two states, either because the transition is too slow to sample or because the force field prefers one state.
Yeah, we already figured this out. Indeed, looking at the histograms of the gyration radius reveal everything we wanted to know at this point. Thanks anyway!