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

[Mark Abraham]

Hi Mahsa,

Thanks very much for your feedback. Those look like useful changes to the
code. Can you please open an issue at https://redmine.gromacs.org with that
information? You'll also be able to attach files, unlike on this list :-)

Mark

On Wed., 12 Jun. 2019, 15:21 Mahsa, <ebadi.mahsa at gmail.com> wrote:

> 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
> >
> >
> --
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