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. Author manuscript; available in PMC: 2015 May 12.
Published in final edited form as: IEEE/ACM Trans Comput Biol Bioinform. 2011 Sep-Oct;8(5):1247–1257. doi: 10.1109/TCBB.2010.104

Fig. 9. RMSD and number of satisfied contacts versus simulation time.

Fig. 9

We folded P4P6 four times, randomizing velocities at the beginning of each stage. We initially folded the P5abc domain separately from the rest of the molecule, then pulled the two domains together after 4.8 ns. From the 2.9 to the 6.7 ns mark, base pairing interactions were turned off for 6 ps periods and back on for 114 ps periods, repeatedly, to escape kinetic traps. This led to the periodic broken contacts in the graph. The contacts were mostly converged after 6.7 ns. Total simulation time was 9.6 ns. In three runs, all 166 base pairing contacts were successfully enforced; in one only 162 were enforced.