This work aims at introducing methods of molecular dynamics (MD) simulation into diffusion MRI modelling. MD allows the study of transport properties (e.g. diffusion), structural properties (e.g. radial distribution functions) and thermodynamic properties (e.g. pressure). Access to all of these properties allows investigation into the links between them. We present the first steps into studying all of these properties (including the diffusion coefficient and kurtosis) in model systems for comparison with MRI data. The system is a binary mixture which includes a diffusing species (the solvent e.g. water) and a larger spatially-fixed species (modelling cellular-sized colloid particles).