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. Author manuscript; available in PMC: 2014 Apr 9.
Published in final edited form as: J Chem Theory Comput. 2013 Mar 11;9(4):1885–1895. doi: 10.1021/ct300978b

Figure 6.

Figure 6

PMF calculation using the self-learning umbrella sampling approach around a predefined string pathway (a) The reaction tube (colored curves) and the location of the initial umbrella sampling windows (red dots) are shown in collective variable space. (b–f) A 2D-PMF is shown for each self-learning umbrella sampling cycle. A free energy value of 3 kcal/mol and a distance value of 30 degrees were selected as thresholds in the self-learning process.