I have built a CG model of a surface on which I want to place a water droplet (some water molecules), and calculate the contact angle. Has anyone done similar work with gromacs (MD simulation)? First, I just want to place some water molecules in a sphere on the surface. Any suggestions?
For generating the droplet, there are two ways. The 'dumb but it works' way is to just generate a box of water adjacent to the surface, and let it equilibrate in vacuum for a time. The box will naturally adhere to the surface and form a spherical droplet after a few 10's of nanoseconds. This has the advantage that you can keep the number of waters equivalent across simulations with different surfaces - just use the same waterbox while swapping out the surface.
The slightly the more complex way is to first generate a regular box on top of the surface. Then, choose a point on the surface to act as the centre of a droplet, and delete any waters that are greater than some distance R (where R is the radius of a sphere). I suggest using VMD or mdanalysis for this task but I'm sure lots of programs can achieve it.
Finally, a trick to improve correspondence with experiment: nano-scale waterdroplets may not accurately represent the contact angle observed in experiment. This is due to the ratio between the distance of the water/surface/vacuum contact line vs the surface area of the interface. To avoid this, one can make the surface periodic with a small cell distance in the x direction (or y), say 1-2nm, so that the droplet forms a cylinder. This makes the contact line linear and removes the effect of so-called 'line tension'. This is described in "On the Water-Carbon Interaction for Use in Molecular Dynamics Simulations of Graphite and Carbon Nanotubes", DOI 10.1021/jp0268112