MD simulations of intermediate Trp-cage structures.

<p>RMSD_Cα of sampled Trp-cage conformations in explicit solvent starting from a set of intermediate structures (a subset of intermediate structures of set2 shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0088383#pone-0088383-g005" target="_blank">Figure 5B</a>,) vs. simulation time with different Amber force fields (A) ff03 (B) ff99SB, (C) ff99SB_ILDN, (D) ff99SB_NMR. All these examples eventually reached a near-native conformation with RMSD_Cα <2 Å from the native Trp-cage structure.