We need to confine polymer chains inside of a nanopore and perform MD dynamics to investigate the favored morphologies. Is this possible with LAMMPS?
If that is not possible, the alternative would be to use a box (or cylinder, or sphere) with non-periodic boundary conditions instead of the nanopore, since we are only interested in polymer-polymer interactions. Is this possible with LAMMPS?
I would greatly appreciate your answers!
Yes, and yes.
But LAMMPS won’t do the building of the systems for you. See: http://lammps.sandia.gov/doc/Section_intro.html#1_3