Skip to main content
. Author manuscript; available in PMC: 2021 Nov 10.
Published in final edited form as: J Chem Theory Comput. 2020 Oct 13;16(11):6763–6775. doi: 10.1021/acs.jctc.0c00273

Figure 7:

Figure 7:

NTL9 folding landscapes based on different coordinates. A PCA landscapes (x-axis PC1, y-axis PC2) at tmol = 0.5, 1.0, 3.0ns constructed from 2D-WE protein folding simulations. Left: Scatter plot of RMSD to folded structure. Middle: haMSM estimated SS distribution −log pSS Right: Difference in haMSM estimated SS distribution and direct transient distribution (at time tmol) from WE −log pSS +log pdirect. Red (blue) shows and increase (decrease) in probability of the SS compared to the direct transient. B VAMP landscapes (x-axis VAMP1, y-axis VAMP2) at tmol = 0.5, 1.0, 3.0ns constructed from 2D-WE protein folding simulations. Left: RMSD Middle: haMSM estimated SS. Right: Difference in haMSM SS and direct transient distribution. 2D images of distributions have been smoothed with a 1 pixel gaussian kernel for visual clarity.