Characterization of a dynamic string method for the construction of transition pathways in molecular reactions.

ABSTRACT: We explore the theoretical foundation of different string methods used to find dominant reaction pathways in high-dimensional configuration spaces. Pathways are assessed by the amount of reactive flux they carry and by their orientation relative to the committor function. By examining the effects of transforming between different collective coordinates that span the same underlying space, we unmask artificial coordinate dependences in strings optimized to follow the free energy gradient. In contrast, strings optimized to follow the drift vector produce reaction pathways that are significantly less sensitive to reparameterizations of the collective coordinates. The differences in these paths arise because the drift vector depends on both the free energy gradient and the diffusion tensor of

SUBMITTER: Johnson ME 

PROVIDER: S-EPMC3406241 | biostudies-literature | 2012 Jul

REPOSITORIES: biostudies-literature