The research in my group focuses on algorithms as well as applications for medium and large scale molecular dynamics (MD) simulations. The application component of this project concerns flow over structured surfaces. Friction of a liquid flowing over a surface, as well as the energetics of wetting are controlled by a nanometer scaling interface region at the surface. To control the properties, molecules can be grafted to the surface. These can affect the interactions and flow of liquids in complex ways. In particular, we are currently interested in the effect of alkane chains grafted onto silica surfaces. Our experimental collaborators from Tokyo Tech have observed complex behavior that changes when modifying the length of alkanes by a few carbon atoms. Slightly longer chains also change behavior when exposed to water over 24 hours. They do not fully understand the behavior and suspect that longer chains somehow group together. This is an ideal case for molecular simulation, as they we can observe processes in atomistic detail and the length scales involved are not too large. The time scales could be an issue, so we will have to try multiple different initial conditions. On the algorithmic side the main project is developing methods for more efficient use of multiple reaction coordinates in enhanced sampling simulations. Enhanced sampling methods have now become mature. Here we use the Accelerated Weight Histogram method, which is developed by my group and implemented in GROMACS. Now that enhanced sampling methods work well, the main challenge that remains is the choice of reaction coordinate(s). This can be a very tough problem and is very system specific. There might exist one ideal reaction coordinate, but that is difficult to find, in particular when one does not know a lot about the process of interest. It would therefore be advantageous to be able to use multiple reaction coordinates to increase the chance of including successful directions. However, this brings back the sampling problem as now a high(er) dimensional space needs to be planned. We will looks for ways to sample more efficiently in this high dimensional space. One thing that can be of help here is the friction metric that is available for the accelerated weight histogram method. The main target for the project are functional motion in proteins. 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.