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Uncertainty control and scalability to large datasets are the two main issues for the deployment of Gaussian process (GP) models within the autonomous machine learning-based prediction pipelines in material science and chemistry. One way to address both of these issues is by introducing the latent inducing point variables and choosing the right approximation for the marginal log-likelihood objective. Here, we empirically show that variational learning of the inducing points in a molecular descriptor space improves the prediction of energies and atomic forces on two molecular dynamics datasets. First, we show that variational GPs can learn to represent the configurations of the molecules of different types that were not present within the initialization set of configurations. We provide a comparison of alternative log-likelihood training objectives and variational distributions. Among several evaluated approximate marginal log-likelihood objectives, we show that predictive log-likelihood provides excellent uncertainty estimates at the slight expense of predictive quality. Furthermore, we extend our study to a large molecular crystal system, showing that variational GP models perform well for predicting atomic forces by efficiently learning a sparse representation of the dataset.