Unrestrained computation of free energy along a path.

ABSTRACT: We apply the adaptive biasing potential (ABP) method to optimize the principal curve defining a conformational transition between two known end states and to subsequently compute the one-dimensional potential of mean force as a function of arc length along the principal curve. This approach allows the use of the ABP method in a collective variable space of arbitrary dimension and offers several advantages over line-search methods. First, configurations are neither generated along an initial path for the transition nor equilibrated during evolution of the path. Second, and most importantly, the powerful sampling provided by the ABP serves to accelerate the dynamics during the optimization and computation of the free energy. Finally, the free energy is formulated as a potential of mean force

SUBMITTER: Dickson BM 

PROVIDER: S-EPMC3697028 | biostudies-literature | 2012 Sep

REPOSITORIES: biostudies-literature