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. 2015 Aug 27;143(24):243101. doi: 10.1063/1.4929598

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Copyright © 2015 AIP Publishing LLC

0021-9606/2015/143(24)/243101/10/$30.00

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FIG. 4. — (a) Native configuration of the V-type Na⁺-ATPase (2BL2) dimer complex visualized using Visual Molecular Dynamics (VMD).³⁰ (b) Free energy profile of the V-type Na⁺-ATPase (2BL2) dimer complex obtained using single memory AWSEM-membrane. The free energy is plotted versus Q_i, the fraction of native interface contacts (x-axis) and the RMSD (y-axis). A representative structure from the free energy basin is shown. The expectation values of (c) the total potential energy, PE, and (d) the contact energy, E_contact, are plotted versus the same order parameters.