Gromacs

Diffusion Constant

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    Version as of 00:43, 7 Dec 2021

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    Using a GROMACS trajectory you can calculate diffusion constants both with Einstein (g_msd) and Green-Kubo (g_velacc and then g_analyze) equations. While g_msd is self-explanatory, using g_velacc starting from the version 4.0 is a bit trickier.

    To calculate the diffusion constant of the particle via Green-Kubo equation the following commands should be supplied:

    g_velacc -acflen 1001 -nonormalize -mol -n atoms.ndx
    

    where 'atoms.ndx' should contain the numbers of the atoms which form the particle of interest. By default, you will obtain 'vac.xvg' with a linear velocity autocorrelation function (VACF).

    Then to obtain the diffusion constant type:

    g_analyze -f vac.xvg -integrate
    

    This will give an integral of the VACF in [nm2/ps].

    Finally, to get the diffusion constant the value should be (by hand) divided by 3 (see Green-Kubo equation) and multiplied by 1000 (converts [nm2/ps] to more usual [10-9*m2/s] or [10-5*cm2/s]).

    Page last modified 19:09, 20 Oct 2009 by JLemkul?