[gmx-users] g_msd and Diffusion Constant

[V.V.Chaban]

which version fo you use?





On Mon, Jul 20, 2015 at 8:28 AM, Ganesh Shahane
<ganesh7shahane at gmail.com> wrote:
> Dear Gromacs Users,
>
> I have performed a simulation of a POPC+Cholesterol bilayer. I wish to know
> the diffusion constant of a particular cholesterol molecule. Towards this,
> I performed a g_msd using the command as follows-
>
> g_msd -f 30chol.xtc -s prod.tpr -lateral z -endfit 800000 -n index.ndx -mol
> chol.xvg
>
> where index.ndx contains a single index for the cholesterol atoms in
> question. In the end, I got 2 different values of diffusion constant, with
> one of them being displayed on the terminal screen and the other value in
> the chol.xvg file.
>
> Does anyone have any idea as to which value should be taken as the value of
> diffusion constant? Any help would be appreciated. Thank you!
>
> --
> Best Regards,
> Ganesh Shahane
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