The immersed boundary method has been widely used in modeling fluid-structure interaction systems. At the length scale of nano-particles, thermal energy of the aqueous environment becomes significant, and the whole system is subjected to thermal fluctuation. The Stochastic Eulerian Lagrangian Method (SELM), an extension of the immersed boundary method, which is integrated with the molecular dynamics software LAMMPS for fluctuating hydrodynamics simulations of fluid-structure interactions is introduced. To capture the thermal and hydrodynamic contributions of the solvent to dynamics, we introduce momentum conserving thermostats and computational methods based on SELM. SELM couples the coarse-grained microstructure degrees of freedom to continuum stochastic fields to capture both the relaxation of hydrodynamic modes and thermal fluctuations. We provide here an overview of the SELM and some applications.