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Bug #2978

Some suggestions about the gmx current tool

Added by Mahsa Ebadi 2 months ago.

Status:
New
Priority:
Normal
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-
Category:
-
Target version:
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Affected version - extra info:
Affected version:
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Description

Hi gmx-developers,

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 equation 9 in this paper:

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

and the pre-factor fit reported in the output of dsp.xvg in my case is:

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

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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