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

[Mahsa]

Hi Mark,

Thank you for your reply!
I opened a new issue with this information in the link you mentioned.

Best regards,
Mahsa

On Wed, Jun 12, 2019 at 10:26 PM Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> 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
> > >
> > >
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>