The optimization algorithm gives the same solution within 0.05 kcalmol when the initial conditions are modified. A detailed study of the optimization algorithm has been carried out in order to check that the final solution does not depend on the initial conditions given to the algorithm.
An ensemble of initial conditions have been selected from the values of the different labs that were unified by SantaLucia  (see Fig. 5.10a). The FDCs predicted by the different energy values are depicted in Fig. 5.10c. Here we can observe how an overestimation (underestimation) in the absolute value of the NNBP energies leads to an overestimation (underestimation) of the mean unzipping force. The same elastic properties (ssDNA, handles and optical trap) have been used in all cases. Figure 5.10b shows the optimal values of the NNBP energies for the ensemble of initial conditions. All the NNBP energies have an error smaller than 0.1 kcalmol.
The optimization algorithm converges to essentially the same solution when starting from various initial conditions because the error bars of the different solutions obtained for each initial condition overlap with each other. Figure 5.10d shows the final theoretically predicted FDCs obtained when using the optimal values of the NNBP energies obtained for each initial condition. The different FDCs are indistinguishable and they reproduce quantitatively the experimental FDC.
JM Huguet 2014-02-12