DescriptionAnalysis of scientific simulation data enables scientists to glean insight from simulations. In situ analysis, which can be simultaneously executed with the simulation, mitigates I/O bottlenecks and can accelerate discovery of new phenomena. However, in typical modes of operation, this requires either stalling simulation during analysis phase or transferring data for analysis. We study the scalability challenges of time- and space-shared modes of analyzing large-scale molecular dynamics simulations. We also propose topology-aware mapping for simulation and analysis. We demonstrate the benefits of our approach using LAMMPS code on two supercomputers.