Translational diffusion of bulk water

LAMMPS LAMMPS General Discussion
1

Hi Axel and lampps users

I need to calculate the translational diffusion of bulk water for T=300K and P = 1atm. Does anyone have a tutorial explaining how to calculate the translational diffusion via lamps or MSD via post-processing?

I need it to answer a referee and I never calculated it.

Thanks

2

Hi @Elizane_Moraes,

There are several ways of doing so and LAMMPS manual has a dedicated how-to section as well as dedicated examples and several discussions archived on the forum.

Adapting a script from the examples to use msd/chunk instead of msd to compute the diffusion constant of water molecules should be rather straight forward.

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Please see Systematic errors in diffusion coefficients from long-time molecular dynamics simulations at constant pressure | The Journal of Chemical Physics | AIP Publishing for potential significant systematic errors in diffusivity of NPT simulations.

As an alternative to @Germain 's excellent answer, in this case I would often export the trajectory into a NumPy data structure with MDAnalysis and directly process the coordinates as numbers-over-time.

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