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. Author manuscript; available in PMC: 2016 Aug 11.
Published in final edited form as: J Chem Theory Comput. 2015 Aug 11;11(8):3714–3728. doi: 10.1021/acs.jctc.5b00271

Figure 3.

Figure 3

DNA GCA hairpin loop MD simulations, starting from B-form and NMR structures. (Top left) Backbone RMSD versus time and RMSD histograms, from GB-HCT simulations starting from 2 conformations. (Bottom left) Backbone RMSD versus time and RMSD histograms, from GB-neck2 simulations starting from 2 conformations. Right: representative structures of most populated clusters from simulations starting from hairpin structures. (Top right) GB-HCT (misfolded). (Bottom right) GB-neck2 (folded, with NMR reference shown in grey). 2nd half of data was used for cluster analysis and histogram calculations.