The glycine receptor (GlyR) is a member of the Cys-loop receptor family of ligand-gated ion channels that is anion selective. The GlyRs play important roles in mediating inhibitory neurotransmission in the spinal cord and brain stem and excitatory neurotransmission in embryonic neurons. Because of their important physiological roles, GlyRs are considered important targets for drug design. The determinants for efficacy of activation of different agonists are, at present, not well understood. In this study, computational modelling techniques including homology modelling, docking, molecular dynamics simulations, and potential of mean force calculations were used to investigate the determinants that confer the efficacy of these compounds at the molecular level in combination with electrophysiology experiments.Homology models of the GlyR1 were built based on the GluCl channel from C. elegans, and the binding modes of different agonists were investigated using docking and MD simulations. The accuracy of our models was validated by site-directed mutagenesis studies in combination with patch-clamp experiments. Our results suggest that the efficacy of the agonists is closely coupled to the energetics of the C-loop of the receptor. With the presence of different ligands in the binding sites, the C-loop closure energy profiles given by potential of mean force (PMF) calculation reveal interesting differences. The results suggest that the combination of modelling and patch-clamp experiments for partial agonists can be a powerful approach to deciphering the atomistic details of glycine receptor activation.