FEARCF a multidimensional free energy method for investigating conformational landscapes and chemical reaction mechanisms

The development and implementation of a computational method able to produce free energies in multiple dimensions, descriptively named the free energies from adaptive reaction coordinate forces (FEARCF) method is described in this paper. While the method can be used to calculate free energies of association, conformation and reactivity here it is shown in the context of chemical reaction landscapes. A reaction free energy surface for the Claisen rearrangement of chorismate to prephenate is used as an illustration of the method's efficient convergence. FEARCF simulations are shown to achieve flat histograms for complex multidimensional free energy volumes. The sampling efficiency by which it produces multidimensional free energies is demonstrated on the complex puckering of a pyranose ring, that is described by a three dimensional W(theta (1), theta (2), theta (3)) potential of mean force.