We present a package using Simulink and MATLAB to perform molecular dynamics simulations of interacting particles obeying a Generalized Langevin Equation. The package, which accounts for three spatial dimensions and rigid-body like rotation, is tuned to explore surface diffusion of co-adsorbed species. The physical parameters are species specific, and include userdefined colored noise spectra and memory friction kernels acting independently on translational and rotational degrees of freedom. We benchmark the simulations using established analytical results for dynamical correlation functions, and we use the package to numerically verify novel analytical results concerning dissipative rotational motion and mutli-exponential friction kernels. The package provides a straight-forward way to expand the modeling of ultra-fast surface diffusion problems at the atomic scale.