This thesis presents the benchmarking and development of a method to study ground state properties of hydrogen clusters using molecular dynamics. Benchmark studies are performed on our Path Integral Molecular Dynamics code using the Langevin equation for finite temperature studies and our Langevin equation Path Integral Ground State code to study systems in the zero-temperature limit when all particles occupy their nuclear ground state. A simulation is run on the first 'real' system using this method, a parahydrogen molecule interacting with a fixed water molecule using a trivial unity trial wavefunction. We further develop a systematic method of optimizing the necessary parameters required for our ground state simulations and introduce more complex trial wavefunctions to study parahydrogen clusters and their isotopologues orthodeuterium and paratritium. The effect of energy convergence with parameters is observed using the trivial unity trial wavefunction, a Jastrow-type wavefunction that represents a liquid-like system, and a normal mode wavefunction that represents a solid-like system. Using a unity wavefunction gives slower energy convergence and is inefficient compared to the other two. Using the Lindemann criterion, the normal mode wavefunction acting on floppy systems introduces an ergodicity problem in our simulation, while the Jastrow does not. However, even for the most solid-like clusters, the Jastrow and the normal mode wavefunctions are equally efficient, therefore we choose the Jastrow trial wavefunction to look at properties of a range of cluster sizes. The energetic and structural properties obtained for parahydrogen and orthodeuterium clusters are consistent with previous studies, but to our knowledge, we may be the first to predict these properties for neutral paratritium clusters. The results of our ground state simulations of parahydrogen clusters, namely the distribution of pair distances, are used to calculate Raman vibrational shifts and compare to experiment. We investigate the accuracy of four interaction potentials over a range of cluster sizes and determine that, for the most part, the ab initio derived interaction potentials predict shifts more accurately than the empirically based potentials for cluster sizes smaller than the first solvation shell and the trend is reversed as the cluster size increases. This work can serve as a guide to simulate any system in the nuclear ground state using any trial wavefunction, in addition to providing several applications in using this ground state method.