Minimum free energy paths

Figure 6 indicates that the drug will first arrive at the minor groove-bound state following the minimum free energy path, i.e. there is a downhill free energy path to the minor groove when the daunomycin approaches the DNA from a completely separated state. 

L. Maragliano, A. Fischer, E. Vanden-Eijnden and G. Ciccotti (2006) String method in collective variables Minimum free energy paths and isocommittor surfaces. J. Chem. Phys. 125, 024106... 

Hu H, Lu ZY, Yang WT (2007) QM/MM minimum free-energy path methodology and application to triosephosphate isomerase. J Chem Theory Comput 3 390... 

The QM/MM minimum free energy path (QM/MM-MFEP) method (122,127, 128) is a free-energy extension to the QM/MM free energy perturbation (QM/MM-FEP) method (123). In the QM/MM- MFEP method, a sequential sampling and optimization procedure is employed in which molecular dynamics simulations are performed for the MM subsystem and geometry optimizations are performed for the QM subsystem. The QM subsystem is optimized on the PMF surface for... 

String Method in Collective Variables Minimum Free Energy Paths and Isocommittor Surfaces. 

Fig. 15.5 2D Free energy surface for the hydride transfer reaction catalyzed by EcDHFR as a function of a chemical and solvent (Se) coordinate (see text for details). The dotted line represents the minimum free energy path and the straight lines correspond to the TS previously obtained just as a function of the chemical coordinate (continuous line) or as a function of both coordinates (dashed)...

L. Maragliano, A. Fischer, and E. Vanden-Eijnden,/. Chem. Phys., 125(2), 024106 (2006). String Method in Collective Variables Minimum Free Energy Paths and Isocommittor Surfaces. 

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