Center-of-Mass of polymer simulation system applying Langevin Dynamics

Ming, I don’t think you can get meaningful chain structure from a single chain, even with PBC. Alot of bad things can happen when the box is too small and the chain interacts with itself. You should probably choose a lengthscale for your chain(s), like R or Rg, and use a box whose sides are larger than that… how much larger is your decision, but there’s plenty of literature to choose from. That might also improve your slow dynamics. There is literature on box size vs diff coeff for unentangled chains- if you want good dynamics, you could use that as a starting point.

good luck,