Interactions between proteins (polymers) and nanostructures (solid surfaces) is gaining increased attention both from the scientific community and the technological standpoint. From nanoelectronics or nanomechanics to system biology, these interactions can bring new features of significance, which have not been well understood. Moreover, with respect to different time scales and size scales in these kinds of systems, e.g. relaxation time of long polymers and carbon nanotubes, numerous complexities occur in simulations of a mixed structure. In this workshop, we would address several important aspects of the simulation of these kinds of structures, including all atoms and coarse grained as well as multiscale modeling. The workshop comprises of two parts. In the theoretical part, some aspects and important issues will be discussed. In the lab section, the simulation of several systems using the Gromacs package will be presented.