[lammps-users] Diffusion coefficient under PBC

Dear all,

Does anyone want to share a method to calculate the diffusion coefficient under periodic boundary condition? I'm running LAMMPS 2004 for protein in hydrated lipids, and have 1000 snapshots(dump atom) of the simulations. I found that my water molecules move from one sim. box to another as time goes, but haven't a clue to obtain a correct way to calculate the diffusion coefficient with Einstein-relationship.

Thanks in advance,

Dept. of Chem. Eng.
TAMU 3122 Texas A&M University
College Station, TX 77840

Hi Kunwoo. If you use LAMMPS's fix msd, you can get
diffusion coefficients out. See: