Molecular dynamics (MD) is a powerful computational tool that paves the way to understand the dynamics and function of life at the molecular level. MD coupled with advanced free energy calculations, and in-silico methods can reveal the underlying mechanism of a physical process that cannot be probed with experimental techniques. The primary investigation in this thesis is to use MD with free energy calculations to explain and elucidate the protein-ligand interactions in glutamate transporters. Glutamate is the major excitatory neurotransmitter in the nervous system and understanding such mechanism may reveal the causes of many pathological conditions linked to glutamate transporters. Here, this thesis presents the results three anomalies observed previously from both experimental and computational studies. First, the instability of a sodium ion bound to the Na2 site observed in simulations is caused by the undercharging of the sulphur atom of the methionine residue in the NMDGT motif. Second, the binding of aspartate to GltPh requires two sodium ions bound in an intermediate state rather than the observed sites revealed from crystallography. Third, the escape of the last sodium ion in the inward-facing conformation shows structural changes in the protein in agreement with experimental observations. An estimate of the escape time from the Na3 site to the bulk indicates this as a slow process in GltPh but is not the rate-limiting step in the transport cycle. As secondary projects, the K+ permeation in gramicidin A (gA) embedded in different lipid membranes and ion solvation in a water droplet is investigated. The potential of mean force (PMF) profile reveals a larger barrier for gA embedded in POPC than in NODS lipid membranes due to the stronger dipole moment of the phosphorus atom. Finally, using spherical boundary condition (SBC) without a buffer zone in the liquid-vacuum interface can give the correct ion-solvation free energy provided a larger system is used.