All-atom simulation of the HET-s prion replication
Fig 2
Comparison between plain MD and biased (rMD and SCPS) trajectories.
In each plot, the Kullback-Leibler divergence between the cross-similarity distribution (Ri) of each iteration i and the self-similarity distribution (A) is shown with blue dots. Each cross-similarity distribution Ri represents the path similarity distribution between the biased and the plain MD reactive trajectories. The self-similarity distribution is the path similarity distribution within the folding events sampled with plain MD. The average Kullback-Leibler divergence between the random cross-similarity distributions (Rr) and the self-similarity distribution is depicted as a red line and it is used as a reference. The random cross-similarity distribution was generated by comparing plain MD simulations with randomly sampled sequences of native contact formation. These results show that both rMD and SCPS produce results that are identical to the one generated with plain MD and are different (with the exception of Trp-cage) from the randomly generated events.