Inside of a cell is highly crowded with a large number of macromolecules together with solvents and metabolites. How proteins or other biomolecules are working in such a cellular environment is one of the most fundamental questions in life science. By integrating data from a variety of sources, we constructed full atomistic model of the cytoplasm of bacteria (Mycoplasma genitalium) with all of the molecular components, i.e., proteins, RNA, metabolites, ions, and solvent, that are mapped on the complete biochemical pathways. The size of the system is 100 nm x 100 nm x 100 nm, which greatly exceeds that of typical molecular dynamics (MD) simulations, covering about 10% of the volume of an entire cell. Using this model, we performed molecular dynamics (MD) simulation with the highly parallelized MD program GENESIS on the super computer K. The simulations provide information of protein dynamics, stability, and interactions. The translational and rotational diffusion of proteins and RNAs are consistent with the reported experimental data. Metabolite dynamics in the macromolecular crowding environments are also investigated and it was found that only few ATPs exist in a bulk solution due to protein-metabolite interactions. The current simulation opens a new era to connect our understanding between molecular and cellular levels in biology.