1. build nano particles in materials studio

2. build water molecular in materials studio

3. use the Amorphouse Cell to construction the nano-water model

3. run a md calculation

My problem is how to generate topology files and parameterize the system. GROMACS can't recognize Si atoms. If you have experience running MD simulations, it would help me a lot if you could explain this to me briefly

For sillica materials, I suggest you use lammps. GROMACS uaually is suit for bio-materials like DNA and has less supported forcefield for non-bio-materials. For non-bio-materials, LAMMPS is good and there are proper forcefield.

For sillica, a cvff forcefield is proper and you may use MS to get the topological data and use MSI2LMP to convert the topological data to LAMMPS's format. You may find an easy tutorial about the convert process.

ps: you could mentional my ID if you have further problems else I could not see. Erfan Nasrollahy