The energetics, structure, and dynamics of two different cations (Na+ and K+), water, and gramicidin A (GA) systems are studied by molecular dynamics methods with parallel computational techniques. The parallel computation techniques employed in this study are described. In our simulations, we study the dynamical behavior of 81 water molecules and a single ion of each kind, placed at one of two different locations along a channel. The ion and water move under the dynamic force fields from each other as well as the static force field of the channel, which is compared of the GA framework constrained to remain the Urry dimer conformation. All force fields are of ab initio origin. The trajectories illustrate the characteristic time scales of typical events at the chosen locations. The velocity and force autocorrelation functions from the simulations (the first computed for any GA model) are discussed.