[gmx-users] Some suggestions about the gmx current tool

[Mahsa]

Hi again,

Something went wrong with the equations which I tried to show.

So for the first equation please see eq. 9 in this paper:

https://aip.scitation.org/doi/10.1063/1.2868752

and the second missing formula is:

1 / 6*V*K_B*T = 7.20677e-12

Best regards,
Mahsa


On Wed, Jun 12, 2019 at 3:12 PM Mahsa <ebadi.mahsa at gmail.com> wrote:

> Hi gmx-users,
>
> I use gmx current tool to calculate static conductivity by version 2018:
>
> gmx current -f md.xtc -o -dsp -md -mj -temp 423 -nojump -n index.ndx -s
> topol.tpr
>
> Indeed the tool is useful, but I think some parts in the output are
> confusing and need to be improved.
> I think the generated dsp.xvg file which reports the MSD of translational
> dipole moments vs time has the wrong unit in the plot. The unit should be
> (S/m) ps according to this equation:
> [image: Screen Shot 2019-06-12 at 14.35.45.png]
> and the pre-factor fit reported in the output of dsp.xvg in my case is:
>
> [image: Screen Shot 2019-06-12 at 14.37.37.png]
> but [(1.6 * 10^-19)^2 * (10^-18)] / [6*V*K_B*T] is equal to 7.20677e-12
> considering the conversion of MSD of dipole moments from (enm)^2 to (em)^2
> so it would be really helpful to add a hint in the documentation or the
> code about that.
> Finally, as far as I understood the reported sigma value in the output of
> dsp.xvg should be multiplied by 10^-12 manually.
> It took sometime for me to understand what is going on in the output :-)
> Please correct me if I'm wrong or missed something in these comments.
>
> Best regards,
> Mahsa
>
>