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. Author manuscript; available in PMC: 2011 Nov 1.
Published in final edited form as: Proteins. 2010 Nov 1;78(14):2922–2934. doi: 10.1002/prot.22815

Figure 1. MD simulation setup and RMSD Analysis.

Figure 1

(A) The structure of ROSETTA-TM herg+3 model after 10 ns equilibration. S5–S6 domains are shown in a green color, S4 is blue and S1–S3 is in magenta (B) the lateral fluctuation of positions for S1–S2 segment along the MD trajectory for ROSETTA-Membrane herg+3 model. (C) RMSD scans along MD trajectory for equilibrated ROSETTA-Membrane herg+3 model. The RMS fluctuations (RMSF) for the pore domain and helical elements are around 2 Å, whereas most flexible elements (EC and IC linkers) display larger fluctuations of up to 4 Å from average structure.