Hi, I would like to ask questions about what we can do with Gromacs. 3. For example I have some different molecules and I would like to see their binding affinity to carbon nanotubes. Is it possible to do this simulation with Gromacs? If possible, I should have attractive and repulsive potentials. Which potential(s) in Gromacs should I use for this purpose? 2. Is it possible to simulate folding mechanism of a protein in closed geometry? closed geometry maybe in cylindrical or cubic shape. 3. Can we check if a protein adhesed or not a to a surface? surface consists of atoms.
Best wishes Mustafa Bilsel
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