[gmx-users] Simulation on a substrate

[Bob Johnson]

Hello everyone,
I am interested in studying the adsorption of single stranded DNA on an infinite
carbon nanotube that is sitting on a silicon dioxide substrate. The substrate
could just be a hard boundary condition for all I care. I would like to have
the nanotube sitting on the substrate and in an aqueous environment. The single
stranded DNA would be floating in the water. Is there a way to do this in
Gromacs? How would the periodic boundary conditions be handled such? The system
is infinite and isotropic in two dimensions. However, in the vertical direction
the system is nonisotropic due to the substrate. Is there a way to simulate
bulk water?
Thanks,
Bob Johnson