[lammps-users] Diffusion coefficient under PBC

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1

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,
Kunwoo.

KUNWOO HAN
Dept. of Chem. Eng.
TAMU 3122 Texas A&M University
College Station, TX 77840
(O)979-862-1079

2

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

http://www.cs.sandia.gov/~sjplimp/lammps/doc/fix_msd.html

Paul