Response to "comment on 'Free energy simulations of single and double ion occupancy in gramicidin A'" [The Journal of Chemical Physics (2008) 128 (227101))

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. © 2008 American Institute of Physics.