Two popular open source software toolkits common for generating large parallel MD datasets are OpenMM and GROMACS . It is worth noting that while GROMACS was originally an acronym for the "GROningen MAchine for Chemical Simulations," the name now is standalone and is no longer an acronym. Below is a brief introduction to each software as well as relevant considerations. Alongside simulation engines, care should be taken in the setup of your system (discussed further below). Many modern engines contain the necessary functions to generate a periodic, solvated, biomolecular simulation system, but it is important to ensure that the starting biomolecule is appropriately constructed (i.e. no missing atoms, expected protein sequence).