Paper Citing NAMD - Abstract
Chen, L. Y.; Bastien, D. A.; Espejel, H. E.
Determination of equilibrium free energy from nonequilibrium work measurements
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 12:6579-6582, 2010
The fluctuation-dissipation theorem (FDT) of Brownian dynamics (BD) is applied to extract the equilibrium free-energy profile from the nonequilibrium, irreversible work measured in single-molecule pulling experiments. Two sets of in silico experiments are performed to explore the free-energy landscape of deca-alanine peptide as a function of its end-to-end distance and to determine the free-energy pro. le of water permeation through the channels of aquaglyceroporin GlpF. With a small number of pulling paths sampled, the BD-FDT is shown to produce accurate estimates of the free-energy profiles for both systems.
