Computing the Free Energy along a Reaction Coordinate Using Rigid Body Dynamics.

ABSTRACT: The calculations of potential of mean force along complex chemical reactions or rare events pathways are of great interest because of their importance for many areas in chemistry, molecular biology, and material science. The major difficulty for free energy calculations comes from the great computational cost for adequate sampling of the system in high-energy regions, especially close to the reaction transition state. Here, we present a method, called FEG-RBD, in which the free energy gradients were obtained from rigid body dynamics simulations. Then the free energy gradients were integrated along a reference reaction pathway to calculate free energy profiles. In a given system, the reaction coordinates defining a subset of atoms (e.g., a solute, or the quantum mechanics (QM) region of a q

SUBMITTER: Tao P 

PROVIDER: S-EPMC4196739 | biostudies-literature | 2014 Oct

REPOSITORIES: biostudies-literature