[gmx-users] Spatially resolved diffusion coefficient

Jacob Alan Spooner Jacob.Spooner at ufv.ca
Thu Nov 22 21:58:38 CET 2018

Dear GROMACS users,

I am interested in obtaining a spatially resolved diffusion coefficient for water in a confined pore system consisting of a slab of metal and water.  My goal is to obtain the xy component of diffusion coefficient (parallel to the metal slab) as a function of distance away from the metal (z).  I am familiar with the ability to calculate D from the msd or the velocity acf in gromacs, but have never been interested in spatial dependence of D. A brief dive into the literature shows me that there are several methods for obtaining a distance dependent D from MD trajectories and these methods vary widely in complexity.  I am wondering if anybody has any experience/success with this type of calculation using GROMACS and could give some advice regarding the most useful tools/methods.

Best Wishes,
Jake Spooner

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