Figure 1.

PCA plot comparing cMD and aMD trajectory sampling for the Ca²⁺-bound system. The principal component space generated by known structures of TnC is shown along with molecular dynamics trajectories that are projected into the first versus second principal component space of known TnC structures. (A) Projections of known pdb structures are shown as filled circles. The NMR structures of 1AP4, 1SPY, and 1MXL are shown as filled green, red, and blue circles, respectively. (B) Projection of the 1AP4 cMD trajectory (full blue circles) into the PC space is shown in density coloring where darker shades of blue indicate the more heavily sampled parts of the trajectory. (C) Projection of the 1AP4 aMD trajectory (full blue circles) into the PC space is shown in density coloring. (D) Projections of the 1AP4 cMD trajectory (full red circles) and the 1AP4 aMD trajectory (full blue circles) into the PC space are shown in density coloring, where darker shades of red and blue indicate the more heavily sampled parts of the trajectories. cMD and aMD trajectories overlap with extended sampling for the accelerated method. Complete overlap of most heavily sampled regions for the aMD trajectory with the cMD trajectory suggests that cMD samples most of the statistically relevant conformations for this system.