Hi GROMACS users, I'm trying to simulate number of esters together with surfactants which experimentally known will self-assembly into micellar aggregates. I don't know if my method is right, but i put these molecules into one pdb file using VegaZZ software. Then if I successfully edited the topologies and managed to run MD simulation on it, are my results valid? Or do I have to specify other parameters/files/options specially for this kind of interactions? Because its a self-assembly process (driven by the hydrophobic effect), I believed there's no need for me to specify which atoms on the corresponding molecules to interact, right? Thanks a lot, Alif.
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