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. 2014 Apr 3;10(4):e1003521. doi: 10.1371/journal.pcbi.1003521

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© 2014 Das et al

This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.

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A. Time trace of the distance between atoms of residues 21 and 256 from a 235 ns long conventional MD simulation of the fully solvated system. The simulation was started from a structure obtained from a targeted MD simulation originated from the OFc state. The system undergoes a spontaneous transition to the IFo state. B. Comparison of the ANMPathway method and all-atom MD in the space of two order parameters. The all-atom MD results are shown as a pseudo free energy landscape , where P is the 2D distribution. The color-scale goes from blue (low energy) to red (high energy). The pathway predicted by ANMPathway (white line) goes mostly through the low energy regions of the free energy landscape.

Inline graphic — A. Time trace of the distance between atoms of residues 21 and 256 from a 235 ns long conventional MD simulation of the fully solvated system. The simulation was started from a structure obtained from a targeted MD simulation originated from the OFc state. The system undergoes a spontaneous transition to the IFo state. B. Comparison of the ANMPathway method and all-atom MD in the space of two order parameters. The all-atom MD results are shown as a pseudo free energy landscape , where P is the 2D distribution. The color-scale goes from blue (low energy) to red (high energy). The pathway predicted by ANMPathway (white line) goes mostly through the low energy regions of the free energy landscape.