Response To "comment on 'free Energy Simulations of Single and Double Ion Occupancy in Gramicidin A' " [j. Chem. Phys. 128, 227101 (2008)]

Abstract

We respond to the criticism that one-dimensional (1D) construction of the potential of mean force (PMF) of ions in channels is flowed. Comparison of the 1D PMF results in the gramicidin A channel with independent free energy difference calculations obtained by using the free energy perturbation and thermodynamic integration methods shows complete agreement, thus providing a justifications for the 1D PMF approximation.