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 liquid mixtures and more realistic surfaces. Both cases enable better comparison with experiments and continuum models, for different reasons. We expect to make significant progress on some unresolved issues in the field. This is done in collaboration with different groups at Mechanics at KTH. A second project concerned the effect of pH on conformations and function of proteins. We have recently developed and implemented efficient algorithms to make protonation states of chosen groups dynamic. The protonation responds to the local environment and the global pH. Even if groups do not show change in protonation states, it is often difficult to predict them. Now we can run simulations and get and observe the correct protonation states, also when they depend of the conformational state of the molecule. One important application i G-protein coupled receptors, which are the largest drug target. Conformational transitions of GPCRs aAll this work in done using the open-source GROMACS molecular simulation package and all algorithmic improvements will be made directly available to the community.re coupled to pH, but it is as of now unclear what the mechanism of this is. 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.