  Steered molecular dynamics (SMD) simulations for the calculation of free
energies are well suited for high-throughput molecular simulations on a
distributed infrastructure due to the simplicity of the setup and parallel
granularity of the runs. However, so far, the computational cost limited the
estimation of the free energy typically over just a few pullings, thus impeding
the evaluation of statistical uncertainties involved. In this work, we
performed two thousand pulls for the permeation of a potassium ion in the
gramicidin A pore by all-atom molecular dynamics in order to assess the
bidirectional SMD protocol with a proper amount of sampling. The estimated free
energy profile still shows a statistical error of several kcal/mol, while the
work distributions are estimated to be non-Gaussian at pulling speeds of 10
{\AA}/ns. We discuss the methodology and the confidence intervals in relation
to increasing amounts of computed trajectories and how different permeation
pathways for the potassium ion, knock-on and sideways, affect the sampling and
the free energy estimation.
