A methodology enabling the robust treatment of model-form uncertainties in molecular dynamics simulations is proposed. The approach consists in properly randomizing a reduced-order basis, obtained by the method of snapshots in the configuration space. A multi-step strategy to identify the hyperparameters in the stochastic reduced-order basis is further introduced. The relevance of the framework is finally demonstrated by characterizing various types of modeling errors associated with molecular dynamics simulations on a graphene sheet. In particular, the ability of the framework to represent uncertainties raised by model reduction and interatomic potential selection is assessed.