I have been using LAMMPS for 3 years now, mainly to simulate polymer cross-linking and biomolecular phase transition. Recently I was curious to know how diffusion of a polymer chain (or a multi-chain cluster) scales with its size. From the short term displacement analysis (MSD vs time plot) done for a single bead/atom (or single chain, or multi-chain cluster), diffusion coefficient (D) is inversely proportional to mass (m) of the object, and proportional to the t_damp parameter that is part of the “fix langevin” command.
Going to the langevin documentation, I found that, viscous drag force is proportional to m/t_damp in the LAMMPS implementation.
Now the question: Since D ~ 1/m, D ~ 1/r^3, where r is the radius of a spherical particle. Stokes-Einstein relation states that D ~ 1/r.
Also, I understand that one can define mass of an atom, but not radius which comes from interaction potentials like LJ. So for an isolated particle, size/radius can not be defined in the input file.
Just wondering whether anyone has any comment on this. Thanks for your time.