The research in my group focuses on algorithms as well as applications for large scale molecular dynamics (MD) simulations. Recently the emphasis of the applications in my group is on molecular aspects of flow and assembly of bio-molecules. In flow there are both fundamental aspects that are not well understood, especially at surfaces, as well as questions about particular applications where molecular aspects become more important due to the smaller scales in micro- and nanofluidics. Although even in nanofluidics most of the system is still best described by continuum (or meso-) dynamics, details of molecular interactions can play an essential role. An important case is the the three-phase contact line in wetting. Molecular processes that can not be described in terms of continuum physics play a crucial role here. Molecular dynamics simulations are the only way to study these effects in detail. Over the past years we have significantly improved the understanding of processes at contact lines. Now we are moving to more complex, and more relevant, cases such as more realistic, as well as more complex surfaces. The quality of the silica(-like) surface has been improved by modelling amorphous silica and annealing surfaces with similar procedures as used in experiments. We will also look into substrates with polymers tethered onto them, although these surfaces are more complex, they are easier to model reliably than amorphous silica surfaces. These simulations will bring us closer to experiments, which enables both better validation of the simulations as well as higher impact, as we expect to the able to find the source of unexplained observations in experiments. This is done in collaboration with different groups at Mechanics at KTH and collaborators at Sorbonne University in Paris and Tokyo Tech. All this work in done using the open-source GROMACS molecular simulation package and all algorithmic improvements will be made directly available to the community.