Sorry for the trivial question, but I am new in Gromacs. I try to simulate a polystyrene film and I want to use a 8.pdb file from an equilibrated film of 32 chains, 80 monomers each. I unterstand that I should enter the residues (for the first, inner and last monomer(s)) and maybe to define the correct parameters in the *.itp file(s). But it is still not clear to me how to define the conectivity between the monomers. Can somebody help me? I saw there are some people simulating polymers with gromacs. Please help!
Thank you for any help, Andrea
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