I am a beginner in Gromacs and currently doing research in petroleum engineering. I want to run some test simulations for the detachment of oil from a rock surface (silica let’s say) in presence of surfactants. But I am not sure where to start. Where can I find the required files, like silica crystal structure and then how to carry out the simulation here. Should I convert my surfactant molecule (drawn in avogadro) into a pdb or is there some other format?
You should post questions in the user forum (User discussions - GROMACS forums). Please note that what you’re seeking to do will require fairly extensive knowledge about most of the inner workings of how GROMACS handles force fields (which will be custom or from some external source) and production of topologies since pdb2gmx is going to be rather useless in your case. You might have some luck with x2top for topology generation but again, that’s somewhat advanced. Do as many tutorials as you can to get up to speed, but honestly, for an application like this, I think you might be better off with LAMMPS or something more common in the materials community.