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Molecular dynamics (MD) simulations allow atomistic insights into chemical and biological processes. Accurate MD simulations require computationally demanding quantum-mechanical calculations, being practically limited to short timescales and few atoms. For larger systems, efficient, but much less reliable empirical force fields are used. Recently, machine learned force fields (MLFFs) emerged as an alternative means to execute MD simulations, offering similar accuracy as ab initio methods at orders-of-magnitude speedup. Until now, MLFFs mainly capture short-range interactions in small molecules or periodic materials, due to the increased complexity of constructing models and obtaining reliable reference data for large molecules, where long-ranged many-body effects become important. This work proposes a general approach to constructing accurate MLFFs for large-scale molecular simulations (GEMS) by training on "bottom-up" and "top-down" molecular fragments of varying size, from which the relevant physicochemical interactions can be learned. GEMS is applied to study the dynamics of alanine-based peptides and the 46-residue protein crambin in aqueous solution, allowing nanosecond-scale MD simulations of >25k atoms at essentially ab initio quality. Our findings suggest that structural motifs in peptides and proteins are more flexible than previously thought, indicating that simulations at ab initio accuracy might be necessary to understand dynamic biomolecular processes such as protein (mis)folding, drug-protein binding, or allosteric regulation.