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.abra...@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.ma...@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.ma...@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-requ...@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-requ...@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-requ...@gromacs.org.
